The problem is that your regex is "greedy": it is matching as far ahead as possible. A negated character class in the regex is one way of dealing with this:

    #!usr/bin/perl -w

    use strict;

    my @lines = qw(
        >sp|P49929|SC52_SHEEP 
        DITCAEPQSVRGLRRLGRKIAHGVKKYG
        >gi|1771590|emb|CAA70562.1| temporin B precursor
    );

    foreach (@lines) {
        if (/^>(\w+)\|([^|]+)/){
            print "$1 == $2\n";    
        }
    }
    
    __END__
    Prints:

    sp == P49929
    gi == 1771590
[download]

Also, if the second field only contains word charcters you could use a simpler match:     /^>(\w+)\|(\w+)/

--
John.