This is one way of doing it:

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

package main;

my @one=('H1', 'H2', 'H3', 'H1', 'H2', 'H3', 'H1', 'H2', 'H3');
my @two=(23, 42, 34, 63, 33, 66, 22, 33, 49);

my %hash = ();

# associate an anonymous array with each hash key.
# initiate the array if key doesn't exist, else
# just push the value onto the key.

for( my $i = 0; $i < scalar @one; $i++ ) {
    unless ( defined ( $hash{$one[$i]} ) ) {
        $hash{$one[$i]} = [ $two[$i] ];
    }
    else {
        push @{$hash{$one[$i]}}, $two[$i];
    }
}

foreach( sort keys %hash) {
    print "$_ : ";
    foreach my $val (@{$hash{$_}}) {
       print " $val ";
    }
    print "\n";
}
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The output is:

~/perl/monks$ ./array-to-hash.pl 
H1 :  23  63  22 
H2 :  42  33  33 
H3 :  34  66  49
[download]