It can be loaded either way. It's totally up to you how you store the info in the hash.

Anyway, here's code that should accomplish your goal.

use strict;
use warnings;

my $fn_assn = ...;
my $fn_pssn = ...;

my @assns;
{
   open(my $fh_assn,  '<', $fn_assn)
      or die("Unable to open assn file \"$fn_assn\": $!\n");

   chomp(@assns = <$fh_assn>);
}

my @pssns;
{
   open(my $fh_pssn,  '<', $fn_pssn)
      or die("Unable to open pssn file \"$fn_pssn\": $!\n");

   chomp(@pssns = <$fh_pssn>);
}

{
   my %pssns = map { $_ => 1 } @pssns;
   my @unique_assns = grep { not exists $pssns{$_} } @assns;

   print("The following ASSNs have no corresponding PSSNs:\n");
   print("$_\n") foreach @unique_assns;
}

print("\n");

{
   my %assns = map { $_ => 1 } @assns;
   my @unique_pssns = grep { not exists $assns{$_} } @pssns;

   print("The following PSSNs have no corresponding ASSNs:\n");
   print("$_\n") foreach @unique_pssns;
}
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thanks, but again have a doubt. I got that my arrays(hashes) have only keys and values are undef. but my flat file is like 1111 2222 3333 4444 which I have loaded into an an hash say %hash1 and I was assuming that with this 1111 and 3333 will become the key for values 2222 and 4444 respectively, but I think I was wrong.

Indeed if you do something like

my %hash=qw/1111 2222 3333 4444/;
[download]

then %hash will have the structure you describe. However generally keys and associated values have a "different nature". Nothing prohibits them to be homogeneus, but I see no reason for them to be so in this case, so is it really what you want?

So I have two flat files just like the above sample and which I have loaded into two separate hashes say %hash1,%hash2, and if they have any not common values/key then store into another array or hash, does not matter. Please help me out...

I wish I could help you but it's hard to make sense of "common values/keys". Also despite your efforts the expression "then store into another array or hash" is still missing the object to be stored into whatever.