The album was produced by Frank Zappa and recorded in March 1969 at Whitney Studios in Glendale, California, following eight months of intense rehearsals at a small rented communal house in Los Angeles.

The lineup of the Magic Band at this time consisted of Bill "Zoot Horn Rollo" Harkleroad and Jeff "Antennae Jimmy Semens" Cotton on guitar, Mark "Rockette Morton" Boston on bass guitar, Victor "The Mascara Snake" Hayden on bass clarinet, and John "Drumbo" French on drums and percussion.

[10] Trout Mask Replica has been widely regarded as the masterpiece of Beefheart's musical career, as well as an important influence on many subsequent artists.

In 2010, the album was selected for preservation in the United States National Recording Registry by the Library of Congress for being deemed "culturally, historically, or aesthetically significant".

In preparation, the band rehearsed Van Vliet's difficult compositions for eight months, living communally in a small rented house in Woodland Hills, Los Angeles.

French recounted living on no more than a small cup of soybeans a day for a month,[15] and at one point, band members were arrested for shoplifting food (whereupon Zappa bailed them out).

Van Vliet once told drummer John French that he had been diagnosed with paranoid schizophrenia, and he would see nonexistent conspiracies that explained this behavior.

Working with Zappa and engineer Dick Kunc, the band recorded some provisional backing tracks at the Woodland Hills house, with sound separation obtained simply by having different instruments in different rooms.

"The Blimp" was recorded by Zappa in his studio while on the phone with Van Vliet prior to the album's sessions; Jeff Cotton was put on the phone to recite Van Vliet's latest poem, which Zappa recorded and put over a Mothers of Invention backing track (which had been known to the Mothers, uncredited on Trout Mask's credits, as "Charles Ives").

"[21] Van Vliet used the ensuing publicity, particularly with a 1970 Rolling Stone interview with Langdon Winner, to promulgate a number of myths which were subsequently quoted as fact.

[22] Van Vliet also claimed to have taught both Harkleroad and Mark Boston from scratch; in fact, the pair were already accomplished musicians before joining the band.

After Van Vliet was finished, French would piece these fragments together into compositions, reminiscent of the splicing together of disparate source material on Marker's tape.

the nose of the wooden mask / Where the holes had just been uh moment ago / Was now smooth amazingly blended camouflaged in / With the very intricate rainbow trout replica."

Some were childhood reminiscences, such as Gene Autry's recording "El Rancho Grande", from which one of the guitar lines in "Veteran's Day Poppy" was adapted, or the "Shortnin' Bread" melody used in "Pachuco Cadaver".

Others were more contemporary, such as the quote "come out to show dem [them]" from Steve Reich's "Come Out" used in "Moonlight on Vermont", or a melodic fragment from the Miles Davis recording of Concierto de Aranjuez used as the basis for the bridge of "Sugar 'n Spikes".

[citation needed] Trout Mask Replica is considered to be Captain Beefheart's magnum opus,[35] and has appeared on lists of the greatest albums of all time.

[38] Lester Bangs, in his original review for Rolling Stone in 1969, hailed the album as "a total success, a brilliant, stunning enlargement and clarification of [Captain Beefheart's] art", and said that, on "a purely verbal level", it is "an explosion of maniacal free-association incantations".

"[40] Steve Huey of AllMusic lauded the album as "stunningly imaginative", and wrote that its influence "was felt more in spirit than in direct copycatting, as a catalyst rather than a literal musical starting point.

[42] The Guardian called the album "the standard by which almost all experimental rock music is judged, its reputation as a fearsomely difficult listen undimmed by the passing of time or its influence.

Cartoonist and writer Matt Groening tells of listening to Trout Mask Replica at the age of fifteen: "I thought it was the worst thing I'd ever heard.

[34] In 2003, Rolling Stone stated that "On first listen, Trout Mask Replica sounds like raw Delta blues", with Beefheart "singing and ranting and reciting poetry over fractured guitar licks.

Tracks such as 'Ella Guru' and 'My Human Gets Me Blues' are the direct predecessors of modern musical primitives such as Tom Waits and PJ Harvey".

"[6] Entertainment Weekly called it "an astonishing, influential onslaught of avant-garde blues that still reveals fresh lunatic nuances on the umpteenth listen.

[56] On January 13, 2012, as part of its "Inside the National Recording Registry" series, the public radio program Studio 360 broadcast a tribute to the album featuring drummer John French, biographer Mike Barnes, and Beefheart devotee Waits.

[61] In an October 1991 interview with Guitar Player magazine, when asked about his influences, guitarist John Frusciante of Red Hot Chili Peppers said, "the most important inspiration is undoubtedly Zoot Horn Rollo's playing on Captain Beefheart's Trout Mask Replica.