The key is realizing that a hash element can store a reference to something else (such as an array). For a good discussion of the technique see perllol. Sample code looks like:

use strict;
use warnings;

my @array1= qw(H1 H2 H3 H1 H2 H3 H1 H2 H3);
my @array2= (23, 42, 34, 63, 33, 66, 22, 33, 49);
my %hash;

push @{$hash{$array1[$_]}}, $array2[$_] for 0 .. $#array1;
print "$_: @{$hash{$_}}\n" for sort keys %hash;
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Prints:

H1: 23 63 22
H2: 42 33 33
H3: 34 66 49
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Also see perlref and perldata.