The answer given by Clemens in 'Life on the Mississippi' is that he took
it from another riverboat man, Captain Isiah Sellers (another familiar
name?) who wrote articles for newspapers and published them under the pen
name 'Mark Twain'.  He was a starchy old fellow who was not much liked by
the younger pilots. Clemens wrote a piece as a parody of the man's style,
and it was his first published newspaper article.  It caused a lot of
mirth amongst the riverboat fraternity, but when Sellers found out he was
deeply hurt, and Clemens immediately regretted what he had done and vowed
that he would use the name 'Mark Twain' as a token of the respect that he
thought the old man was due, till his dying day.
 
 
Best regards
Graham