So now I have got keys and values.

You may think you do, but you don't. Post runnable code ala How do I post a question effectively?, like

#!/usr/bin/perl --
#~  2011-07-05-05:39:58 Anonymous Monk
#~ http://perlmonks.com/?node_id=912812# Read file in a hash and compa
+re the 'values' from file 2
#~  perltidy -csc -otr -opr -ce -nibc -i=4     
use strict;
use warnings;
use autodie;
use Data::Dumper qw/ Dumper /;
use 5.010;

Main(@ARGV);
exit(0);

sub Main {
    if ( @_ == 2 ) {
        NotDemoMeaningfulName(@_);
    } else {
        Boobbly();
        print Usage();
    }
} ## end sub Main

sub NotDemoMeaningfulName {
    my ( $inputFile, $outputFile ) = @_;
    open my ($inFh),  '<', $inputFile;
    open my ($outFh), '>', $outputFile;
    my $d;
    my $read;
    my %hash;
    while (<$inFh>) {
        $d = $_;
        $read .= $d;
        my ( $key, $val ) = split /\n/, $read;
        $hash{$key} = $val;
    } ## end while (<$inFh>)
    print $outFh Dumper( \%hash );
} ## end sub NotDemoMeaningfulName

sub Usage {
    <<"__USAGE__";

$0    inputfile  outputfile

__USAGE__
} ## end sub Usage

sub Boobbly {

#~ http://perlmonks.com/?abspart=1;displaytype=displaycode;node_id=912
+812;part=1
    my $Furrry = <<'__Furrry__';
>1       ##key
abcdef   ##value
>2
hijkl
>3
abnikhl..etc
__Furrry__

    NotDemoMeaningfulName( \$Furrry, \my $Farts );
    print $Farts, "\n\n";
} ## end sub Boobbly

__END__
$VAR1 = {
          '>1       ##key' => 'abcdef   ##value'
        };
[download]

Also read these FAQ items

How can I tell whether a certain element is contained in a list or array?

How do I compute the difference of two arrays? How do I compute the intersection of two arrays?

How do I test whether two arrays or hashes are equal?