What you want to create is a hash of arrays. Your code was close, although I'm not sure why you split $seq again... (unless $seq contains a list of items you need to break out, in which case you want a hash of arrays of arrays). Something like this should work:

while (<MYFILE>) #this is my opened file
{
  {                   
    next if /^\s*File/; #remove line starting with filename

    my ($id, $seq) = split; # The my is important  
    push @{$species{$id}}, $seq;        
  }        
}

# later...

while ( ($key, $sequence) = each %species ) {
  print $key, "\t", join ":", @$sequence;
}

# Which will out your key, followed by a tab, 
# followed by all your sequences (however many 
# there are) separated by colons
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Refer to perlman:perlref for more details on references and why they're a good thing. If you need a hash of arrays of arrays that's not a problem, but it complicates the assignment and de-referencing of your hash, and is an exercise left to the reader. :-D

Gary Blackburn
Trained Killer

Edited: after re-reading what the poster really wanted.