Parts of this FAQ have been superceded by the song history, which has been edited (and vetted) recently, though is focusedon the song and thus perhaps not as comprehensive as this page.
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Source: This is an old Mustangs song, originally written by Cyril Ferguson. Mike went on a Carribean vacation and saw the Mustangs perform in Freeport, then bought the album (tape?) and brought it home. "Ya Mar" (sometimes written "Yamar" by fans) was on the tape (purportedly the only tune on it worth covering), though the Mustangs are guessed to have covered it from someone else. (Thanks to Julia "FahtHarpua")

Lyrics:

• Spanish?: Whether it's "Yamar" or &quotYa Mar", the words and title could be Spanish. Note that "llamar" is Spanish for to call; the Mustangs' spelling, then, might corrupt an earlier version, with interesting consequences for the lyrics, either in reference to the song Llama or with the chorus translated "To call, to call, to call, to call, to call, to call, to call, I call your Pa." Alternately, Gus Birdsey emailed 6/20/96 to say that "'Ya' means 'anymore' in Spanish and 'Ma' means 'sea' in Spanish. I don't think this is what Phish meant [though it could refer to the singer's father going out to sea?] but just a thought."
• Hebrew? Dupree318 reported (8/3/98) that yamar means "he will say" in Hebrew.
• Marley?: Jeff Sapyta emailed (9/18/95) saying the song is about Trey's dog Marley. He mentions "an '87 show at a party for 'the people that took care of Marley while we were on tour'. And in it they have a little thank you section and an explanation and then they play 'Ya Mar'. I always thought it was Ya Mar^7 and then "ya no good dog!"" David Petrozzi posted (8/23/97) about 8-21-87, which has a version "that is slowed down a lot. You can distinctly hear the chorus: 'Yamar, Yamar..... you no good dog'. Trey even mentions Marley's name in the song as well (fitting since he was barking throughout the show... Marley that is)." Note that this might be an explanation for their source of interest in the song, but not what they actually sing; or it could be something sung since that date (or on particular dates since) but not what they've always sung; etc. Remember the flux.
• The rest of 'em sometimes very (eg he vs you), but basically:

  Remember all the times... in the pond catching wild trout... 'til the break of dawn now that he's [you've] become a man... he's [you're] looking very mean he's [you] got a nice shiny sports car... he keeps [you keep] it very clean don't ask him [you] what it was... tell him [me] what it is  (x2)  Ya Mar  (7x)   Ya no good pa  She used to be a very good [vampire?] child... walking in the yard now that she's become a woman...she's looking very proud she used to wear a piece of cloth...tied around her head now she looks so good lord...want to love you dead [what a lovely day]  don't ask her what it was...tell her what it is  (2x) 

Leo: Trey often yells "Play it LEOOOOOOOOOOO!" just before the big keys jam. (Fishman also joins in, e.g. "Go Leo go!" at 12-6-97. As Andrew Van Alstyne posted (8/23/97), Leo is yelled in other songs as well, including Harpua and NICU. And Mike yelled that same line to Leo Kottke during his Fall 2002 tour, when the duo covered "Yamar". And at 2/28/03, Trey yelled "Play it Leo... Kottke".

Cassius posted (8/23/97) that, "Leo was (is?) the keyboard player for the Mustangs the caribean band responsible for the tune Ya Mar. Apparently on the recording the band had, during the keyboard break the band encourages Leo to get down. Thus Trey copies the Mustangs and Leo became another name for Page. Now [can anyone explain] the whole Ya Mar incident from 8-24-93, something about Mike 'rectifying' fingers"?

Similars: Mark Toscano reported (2/24/99), "listening to a dub CD by Mad Professor called The Lost Scrolls of Moses, and track #11 'Bugle SocA' is basically Ya Mar, dub-style!""

Thanks also to Christian David Hoard Lisbeth Karpman, James Noonan, Aaron Klinger, and Glerin Fitzpow.