oh well, the splitting part works as you see. The problem is the overwritten hash in this case. But your tip also makes my code better, thanks for that!

D'oh! Late waking up this morning. That's because hashes can only have unique keys... you can create a hash of arrays to fix this issue:

#!/usr/bin/perl
use warnings;
use strict;

use Data::Dumper;

my %h;
my @a;

while (<DATA>){
    chomp;
    my @a = split /@@@/;
    push @{ $h{$a[0]} }, $a[1];
} 
print Dumper \%h

__DATA__
CustomerA@@@DomainA
CustomerA@@@DomainB
CustomerA@@@DomainC
CustomerA@@@DomainD
CustomerA@@@DomainE
CustomerB@@@DomainA
CustomerB@@@DomainB
CustomerB@@@DomainC
CustomerB@@@DomainD
CustomerB@@@DomainE

__END__
$VAR1 = {
          'CustomerB' => [
                           'DomainA',
                           'DomainB',
                           'DomainC',
                           'DomainD',
                           'DomainE'
                         ],
          'CustomerA' => [
                           'DomainA',
                           'DomainB',
                           'DomainC',
                           'DomainD',
                           'DomainE'
                         ]
        };
[download]

Then access everything like this:

for my $key (keys %h){
    for my $elem (@{ %h{$key} }){
        print "$key: $elem\n";
    }
}
[download]