The members of the original Magic Band had come together in 1965. At this time Van Vliet was simply the lead singer of the group, which had been brought together by guitarist Alex St. Clair. As in many emerging groups in California at the time, there were elements of psychedelia and the foundations of contemporary hippie counterculture.

Thus, it seemed quite logical to promote the group as "Captain Beefheart and His Magic Band", around the concept that Captain Beefheart had 'magic powers' and, upon drinking a 'Pepsi', could summon up "His Magic Band" to appear and perform behind him. The strands of this logic emanating from Vliet's Beefheart persona having been 'written in' as a character in a 'teenage operetta' that Zappa had formulated, along with Van Vliet's renowned 'Pepsi-moods' with his mother Willie Sue and his generally spoilt teenage demeanor.

In late 1965, after numerous car-club dances, juke joint gigs, appearances at the Avalon Ballroom and winning the Teenage Fair 'Battle of the Bands', the group finally bagged a contract for recording two singles with the newly-created A&M Records label with Leonard Grant as their manager. It was at this time that musical relationships had also been struck with members of Rising Sons who would later feature in the band's recordings. The A&M deal also brought some contention between members of the band, torn between a career as an experimental 'pop' group and that of a purist blues band. Working with young producer David Gates also opened up horizons for Vliet's skills as a poet-cum-lyricist, with his "Who Do You Think You're Fooling" on the flipside of the band's first single, a cover of the Ellas McDaniel/Willie Dixon-penned hit, "Diddy Wah Diddy". Fate and circumstance, not for the first time, would befall the band's success upon its release - which coincided with a singles cover of the same song by The Remains. The initial line-up of the Magic Band that entered the studio for the A&M recordings was not that which emerged by the second release, "Moonchild", also backed by a Vliet-penned number, "Frying Pan". A 12" vinyl 45rpm mono EP was later released in 1987, with the four tracks of the two singles, plus "Here I Am, I Always Am" as a fifth previously unreleased song. This release was titled The Legendary A&M Sessions, with a red-marbled cover and (later) members Moon, Blakely, Vliet, Snouffer and Handley seated in a 'temperance dance band' photo-pose.

The original Magic Band was primarily a rhythm and blues band, led by local Lancaster guitarist Alexis Snouffer, along with Doug Moon (guitar), Jerry Handley (bass), and Vic Mortenson (drums), the last being rotated with and finally replaced by Paul Blakely, known as 'P.G. Blakely'. For the first A&M recording Mortenson had been called up for active service and Snouffer stood in on drums, with a recently recruited Richard Hepner taking up the guitar role. By the time the single was aired on a pop television show P.G. Blakely was back in the drum seat. He then left for a career in television and was replaced by John French by the time the band cut their first album, as the first release on the new Buddah Records label.

Personnel in the Magic Band for Beefheart's first album, Safe as Milk, were Alex St. Clair, Jerry Handley and John French. Earlier meetings with the Rising Sons had also secured them the guitar and arranging skills of Ry Cooder, which also brought about input from Taj Mahal on percussion and guitar work from Cooder's brother-in-law Russ Titelman. Further guests to this line-up included Milt Holland on percussion and the all-important and controversial theremin work on Electricity by Dr Samuel Hoffman. It was perhaps this track, above the others, which caused A&M to view the band as 'unsuitable' for their label with what was seen as weird and too psychedelic for popular consumption. Thus, this album was recorded for Buddah, with the band signed to Kama Sutra, which left them close to penniless after extricating themselves from A&M. A large proportion of the tracks on this album were co-written with Van Vliet by Herb Bermann, whom Vliet initially met up with at a bar gig near Lancaster. Part-time Hollywood television actor and budding scriptwriter Bermann and his then wife Cathleen spent some time in Vliet's company prior to this release. Bermann would later write for Neil Young and script an early Spielberg-directed television medical drama. Gary 'Magic' Marker (the "Magic" added by Beefheart) was involved in early session work for this release, and his involvement with Rising Sons was also instrumental in acquiring the skills of Cooder, upon an unfulfilled suggestion that Marker might produce the album. Marker would later lay down two uncredited bass tracks for Trout Mask Replica before being replaced by Mark Boston.

French worked on five more Beefheart albums, while Snouffer worked with Beefheart on and off on three more albums. Bill Harkleroad joined the Magic Band as guitarist for Trout Mask Replica and stayed with Beefheart through May 1974.

While appearing humorous and kind-hearted in public, by all accounts Van Vliet was a severe taskmaster who abused his musicians verbally and sometimes physically. Vliet once told drummer John French he had been diagnosed as a paranoid schizophrenic and thus he would see inexistent conspiracies that explained this behaviour. The band were reportedly paid little or nothing. French recalled that the musicians' contract with Van Vliet's company stipulated that Van Vliet and the managers were paid from gross proceeds before expenses, then expenses were paid, then the band members evenly split any remaining funds—in effect making band members liable for all expenses. As a result French was paid nothing at all for a 33-city U.S. tour in 1971 and a total of $78 for a tour of Europe and the U.S. in late 1975. In his 2010 memoir Beefheart: Through The Eyes of Magic French recounted being "screamed at, beaten up, drugged, ridiculed, humiliated, arrested, starved, stolen from, and thrown down a half-flight of stairs by his employer".

The musicians also resented Van Vliet for taking complete credit for composition and arranging when the musicians themselves pieced together most of the songs from taped fragments or impressionistic directions such as "Play it like a bat being dragged out of oil and it's trying to survive, but it's dying from asphyxiation." John French summarized the disagreement over composing and arranging credits metaphorically:

If Van Vliet built a house like he wrote music, the methodology would go something like this... The house is sketched on the back of a Denny's placemat in such an odd fashion that when he presents it to the contractor without plans or research, the contractor says "This structure is going to be hard to build, it's going to be tough to make it safe and stable because it is so unique in design." Van Vliet then yells at the contractor and intimidates him into doing the job anyway. The contractor builds the home, figuring out all the intricacies involved in structural integrity himself because whenever he approaches Van Vliet, he finds that he seems completely unable to comprehend technical problems and just yells, "Quit asking me about this stuff and build the damned house."... When the house is finished no one gets paid, and Van Vliet has a housewarming party, invites none of the builders and tells the guests he built the whole thing himself.
Post-Beefheart, receiving only a "grumpy" reception from him, the band reformed in 2003 with John French on lead vocals, Gary Lucas and Denny Walley on guitars, Rockette Morton on bass, and Robert Williams on drums. At the start of their only European tour, Williams left and was replaced by Michael Traylor. The band released two albums and toured before disbanding in 2006.

They toured the UK in 2005, playing a selection of small venues. John Peel was initially skeptical about the re-formed Magic Band. He played a live recording of the band recorded at the 2003 All Tomorrows Parties festival on his radio show; afterwards he couldn't speak and had to put on another record to regain his composure. Later the band did a live session for him. The band's albums are Back to the Front (on the London-based ATP Recordings, 2003) and 21st Century Mirror Men (2005). They played over 30 shows throughout the United Kingdom and Europe, and one in the United States. They have been chosen by Jeff Mangum of Neutral Milk Hotel to perform at the All Tomorrow's Parties festival that he will curate in March 2012 in Minehead, England.

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