Jon Spencer and Cristina Martinez first met in 1985 at a gig by The Jesus and Mary Chain in Washington, D.C., where both were living. Spencer had already formed the seminal noise-rock band Pussy Galore, which soon moved from D.C. to New York, accompanied by Martinez, mainly due to her romantic interest in Spencer, although she also enrolled in a film course at New York University. Martinez was soon to drop out of her course and join Pussy Galore as 3rd guitarist, despite her lack of musical experience. Bob Bert was the drummer in the early Boss Hog.

Pussy Galore were plagued by inter-band arguments, notably involving Martinez and second guitarist Julie Cafritz. Martinez left the band in 1987 but the arguments continued. The band eventually split up in 1990, by which time Spencer and Martinez had married.

Boss Hog was formed in 1989, as something of an accidental side project, when Jon and Cristina were told of a last minute vacancy on the bill at the influential New York punk club CBGB's. The pair put together a group of musicians from members of The Honeymoon Killers and Unsane, along with Kurt Wolf from Pussy Galore. The gig is reported to have been an underground sensation in New York, not least because Cristina performed the whole show naked.

The same line-up of Spencer, Martinez, Charlie Ondras, Jerry Teel and Kurt Wolf recorded the mini-album Drinkin', Lechin' & Lyin' for the record label Amphetamine Reptile in 1989. Martinez continued the sexual notoriety by appearing on the cover naked save for thigh-length black leather stilletto boots and arm-length black leather gloves.

The line-up of the band became highly unstable in the early '90's with members rapidly arriving and departing. Pete Shore of Unsane joined on bass and the band did a few dates on the east coast with the Laughing Hyenas. The band recorded their first full-length album Cold Hands in 1990. Once again, the cover featured a nude Martinez, although this time in a more tasteful and non-explicit pose. These first two releases are now long-deleted and are rarities on the collectors' market.

After recording "Cold Hands" Pete Shore and Jerry Teel left the band and Jens Jurgensen joined on bass in order to tour Europe to promote the record. This lineup recorded the BBC Radio session and additional tracks that were released as the "Action Box" double single. Shortly thereafter Kurt Wolf left the band and Marcellus Hall of Railroad Jerk joined on guitar for another European tour and to record the track "Fire Of Love" for a Sub Pop single compilation called "Smells Like Smoked Sausages." During the next year drummer Charlie Ondras died of a heroin overdose.

The band took a break for over two years, whilst Spencer concentrated on the Jon Spencer Blues Explosion, prior to emerging in 1993 with a new, stable line-up of Spencer, Martinez, Jurgensen and Hollis Queens. The new line-up recorded the Girl + EP with Martin Bisi. It met with some critical acclaim, especially for lead track "Ruby", and proved to be a turning point for the band's fortunes. They went on to sign a deal with David Geffen Company. A joke band biography that was circulated by Geffen Records fictitiously claimed Jurgensen came from Swans, which is often misreported as fact.

Their 1995 major-label debut was simply entitled Boss Hog and featured toned-down cover art in which Martinez appears only as a black-clad cartoon holding an umbrella. Within, the sleaze-glam punk sound of abrasive buzzsaw guitar and part sneering, part shouted vocals continued largely unabated. The band toured to promote this release in Europe, Japan and Australia as well as the US, reportedly the first time they had toured for more than a fortnight at a time.

The band made a brief appearance as themselves in the 1996 movie Joe's Apartment. After this, they took another extended break whilst Spencer and Martinez had their first child together, a son, named Charles, in honor of former bandmate, Charlie Ondras.

In 2000, Boss Hog re-emerged with the Whiteout album (released in Japan in 1999), adding keyboard player Mark Boyce to the lineup, who had toured with the band after the Geffen Record. The album featured a typically minimalist sound and a strong visual statement, with the band dressed in all-white. Parenthood proved no barrier to restoring the levels of glamour and sexual provocation, within a more polished sound. This time, the album was released on two record labels, with different cover art for different territories. On both covers Martinez posed against an all-white backdrop, in one wearing white underwear and on the other topless with long hair extensions.

The success of Whiteout was accompanied by a number of singles and gigs and a flurry of publicity, before the band went silent again.

Boss Hog has given no official statement of their disbanding. Jon Spencer continues with the Blues Explosion and is still married to Cristina Martinez. Hollis Queens put together her own band, Lo-Hi, in which she was the singer and played guitar rather than drumming. Lo-Hi released two albums, ...Kind Of Like A Feel Good Thing (1998) and Say It More (2002). Mark Boyce has been touring with G. Love and Special Sauce, and is credited in the group's 2006 album Lemonade.1

Boss Hog played their first show in 8 years on December 3, 2008 at Maxwell's in Hoboken, New Jersey.