San Diego’s Haunted Museums

Posted: 03.18.2021 | Updated: 05.07.2025

Filled To The Brim With Haunted History 

Museums capture the hearts of those who wander through their halls, offering a sanctuary for the stories, relics, and memories of the past. With over 35,000 museums across the United States—and more than 1,000 in California alone—it’s clear that history has a stronghold in our culture.

Affectionately known as “America’s Finest City,” San Diego stands out not only for its beauty but also for its rich and mysterious history. Founded in 1769, San Diego is the oldest city in The Golden State, predating California’s statehood by over 80 years. With more than 35 museums in the city, it’s no surprise that some of them are home to more than just dusty artifacts—they’re also home to lingering spirits.

Among the most notable haunted museums in San Diego are the Whaley House and the Villa Montezuma, each offering ghostly tales and unexplained phenomena. These locations are not just historical landmarks but also infamous San Diego haunted houses, drawing thrill-seekers and history lovers alike. Whether you’re on a San Diego ghost tour or just exploring at your own pace, don’t miss the chance to step inside a truly chilling haunted house San Diego has kept alive for generations.

Uncover the city’s dark secrets with a spine-tingling ghost tour through San Diego’s most haunted hotspots.

Which San Diego Haunted Houses are also Museums?

If you’re seeking a spine-chilling blend of history and hauntings, several haunted museums in San Diego offer just that eerie thrill. The Whaley House in Old Town San Diego stands out as both a historic museum and one of the most infamous San Diego haunted houses—a must-see stop on any San Diego ghost tour.

This haunted house in Old Town San Diego is steeped in tales of tragic deaths and restless spirits. Another chilling spot is the Davis-Horton House Museum in the Gaslamp Quarter, known for its paranormal activity and rich Victorian history.

These haunted museums not only preserve San Diego’s past but also give you a close encounter with its ghostly legends. Ready to step into a haunted house San Diego style? These eerie destinations deliver both chills and culture.

Would you like a map or tour schedule for these haunted spots?

Whaley House Museum

Built back in 1857, the Whaley House has many tales to tell. Located on namesake street San Diego Avenue, the house was the home of Thomas Whaley and his family. A beautiful old gem, built right atop a graveyard.

No harm is done there, right? It also once existed as a general store, a county courthouse, as well as the first commercial theater in San Diego. Residents to the area state that the house has ‘witnessed more history than any other building in the city.’

So, who was Thomas Whaley? Mr. Whaley was born in NYC, later moving to San Francisco during California’s gold rush, and found himself settled in San Diego in 1851.

After marrying Anna Eloise, he and his new wife had six children here at the house. One of his children died from scarlet fever in the home at 18 months, and after a 9-year sabbatical in San Francisco, his family moved back into the San Diego home.

Thomas’s daughters, Violet and Anna, were both married in Old San Diego.  Violet married a man named George Bertolacci, and Anna married her first cousin, John Whaley. (Times were strange back then, it seems.)

While Anna’s marriage was odd, Violet’s marriage was downright horrific. Two weeks into her marriage, she awoke to her husband gone.

Bertolacci, it turned out, was an incredible con artist and only married Violet to receive the substantial dowry. After she returned home unchaperoned, she was shunned by her society since this was something’ proper 19th century ladies should never do.’

Violet and George’s divorce became finalized about a year later, but Violet never recovered from the public humiliation and betrayal. Her depression got the best of her on August 18th, 1885, when she shot herself in the chest with Thomas’ 32-caliber gun. She did leave a truly chilling suicide note…

‘Mad from life’s history,

swift to death’s mystery,

glad to be hurled,

anywhere, anywhere, out of this world.’

-Violet Whaley

Shortly after Violet’s death, the Whaley family fell into disrepair. Thomas fell ill at the home and died. Her sister’s engagement was broken off due to the scandal that Violet’s death caused.

In late 1909, the Whaley House remained vacant and began to rot. Francis Whaley undertook the restoration of the home and turned it into a tourist attraction. After the history of deaths in the house, it remains well known as a local haunted hotspot.

It is said that guests and staff will catch glimpses of apparitions of those who took their final breaths within the walls of the home, baby Thomas Jr., Violet, and Thomas Sr. In 2005, LIFE magazine called the Whaley House ‘The Most Haunted House in America.’

Even the Whaley family themselves experienced hauntings in the home. They began hearing the footsteps of a man they claimed to be ‘Yankee Jim’ who was hanged on the property for stealing a boat.

Today, more than 30 restless spirits are believed to inhabit the Whaley House, making it one of the most famously haunted museums in San Diego. From long-lost family members to mysterious strangers—and even a ghostly fox terrier named Dolly—this haunted house in Old Town San Diego is brimming with paranormal activity.

As you explore the Whaley House Museum, keep your senses sharp; those who died within its walls may still be lingering. Whether you’re a history buff or a thrill-seeker, this legendary stop on a San Diego ghost tour offers a hauntingly unforgettable experience. Among all San Diego haunted houses, few blend eerie history and ghostly presence quite like this haunted museum.

 Villa Montezuma Museum

The Villa Montezuma Museum was built in 1887 and was once a mansion to Jesse Shepard, who is said to haunt the building. He was a pianist and spiritualist who sat at his piano bench and claimed to channel famous composers.

Sitting on San Diego’s outskirts, the home is now a historical landmark and has been named one of San Diego’s most haunted houses. Just looking at the home itself shows you the strange fascinations and eclectic tastes that Jesse had.

Stained glass windows lining the home, gargoyles perched around on the tallest parts, and five fireplaces can be found inside. Jesse also had a tower built that was used as his study and an entire east wing set aside for his love of music.

Due to Jesse’s affluent tastes, he had many connections that would eventually draw the attention of those interested in the paranormal. He found himself holding séances in the home with his closest friends. During these gatherings, Jesse believed that he had the power to open doors and a line of communication with the dead.

Many of his friends thought he was successful in contacting spirits during these séances. People on the streets started to hear full orchestras playing at night when Jesse was the only one home! Residents began to believe that he was playing with a ghastly orchestra!

These days, several spirits are said to haunt the Villa Montezuma. While details are scarce, one spirit is said to be of a man who hanged himself from the second-floor observatory, and another is said to be a former owner of the mansion. Multiple visitors have seen a hanging apparition, disembodied voices, and phantom music echoing throughout the large home.

Interestingly enough, none of the villa’s many owners have ever found success in their lives while living there. Each of them faced severe and life-changing financial ruin and was forced the sell the Villa to someone else. It is rumored that the Villa Montezuma has had a curse placed on it that guaranteed the quick decline of all who moved into it.

The poltergeist of Jesse Shepard himself is also said to play his piano here when the house is empty; passersby can hear the keys tinkling from inside the dark mansion. Tourists to the museum confirm the Villa’s eerie vibe, and many have also reported seeing ghostly figures and faces in the colorful stained glass windows. One face, in particular, seems to capture the attention of eyewitnesses the most, Flemish artist Peter Paul, whose ghostly beard can be seen graying more and more as each year passes.

What is genuinely most astounding about the hauntings at Villa Montezuma is the manner in which Jesse Shepard died. He was with his roommate, Lawrence Tonner, like any other night, playing the piano for guests. After striking the last key to finish his piece, he died.

No one had noticed until they realized that Jesse was unresponsive to their adoration and praise. Tonner approached the bench and soon realized that Shepard was completely frozen with his hands still on the keys. Even though Jesse did not die in the Villa, he died in Los Angeles, and it is said that his spirit returned here due to his love and attachment for the Villa.

Today the Villa Montezuma is open to the public to visitors who register with the San Diego Parks and Recreation department. Free tours are given four times a year to all who gather.

Museums hold the key to understanding our past, preserving stories and relics that define generations. In San Diego, some of these museums do more than just educate—they haunt. The Whaley House, a haunted house in Old Town San Diego, and the Villa Montezuma are two standout haunted museums that bring history to life… and perhaps a few spirits with it. These San Diego haunted houses are popular stops on any San Diego ghost tour, offering both chilling stories and historic insight.

And if your ghost-hunting adventure runs late, why not spend the night somewhere just as spooky? Check out our guide to haunted hotels in San Diego—you might end your night with even more ghost stories to tell.

Haunted San Diego

If San Diego’s haunted museums have stirred your curiosity, you’re in for a chilling adventure. These historic landmarks are brimming with eerie legends, unexplained phenomena, and the lingering presence of souls from long ago. The sorrow and mystery woven into these haunted sites rival the ghost stories whispered throughout the city, offering a spine-tingling glimpse into the darker side of San Diego’s past.

Want more goosebumps? Head over to our blog for even more haunting tales, and start mapping out your next San Diego ghost tour. Be sure to follow us on Facebook, Instagram, and TikTok to stay up to date with all the latest haunted happenings!

Sources:

• https://theresandiego.com/31-photos-prove-san-diego-americas-finest-city/
• https://sandiegohistory.org/archives/biographysubject/whaley/
• https://sandiegohistory.org/journal/1970/july/shepard/
• https://www.nbcsandiego.com/news/local/the-whaley-house-gets-into-the-halloween-spirit/51451/