Could you please take a look at this and let me know if there's any logical error? I think it works well.. Also if you can give me any suggestions, please do not hesitate to reply / message. Thank you so much!! (***Special thanks to BioLion! You're awesome :D***) 
#!/usr/bin/perl
use warnings; # Perl interpreter command
use strict;


my %bow1 = ();
my $file1 = shift;
open (FILE1, "$file1")|| die "Failed to open $file1 for reading : $!";
+ # Open first file

while (<FILE1>) { # Reading first hash
    my ($ID, undef, undef, undef, $Seq) = split;
    $bow1{$ID}[0] = $ID;
    $bow1{$ID}[1] = $Seq;
}
close FILE1 || die "Failed to close $file1 : $!";


my %bow2 = ();
my $file2 = shift;

open (FILE2, "$file2") || die "Failed to open $file2 for reading : $!"
+; # Open first file

while (<FILE2>) { # Reading second hash
    my ($ID, undef, undef, undef, $Seq) = split;
    $bow2{$ID}[0] = $ID;
    $bow2{$ID}[1] = $Seq;
}
close FILE2 || die "Failed to close $file2 : $!";


print"Match status\t$file1 ID\t$file1 Sequence\t$file2 ID\t$file2 Sequ
+ence\n"; # Print title

my $totalCount=0; #initialize variables for counting
my $identical=0;
my $diffSeq=0;
my $unique=0;

foreach my $ID (keys %bow1){ # can use (sort keys %hash) to put items 
+in a specified order
   if (exists $bow2{$ID}[0] ){
      if ( $bow1{$ID}[0] eq $bow2{$ID}[0] ){
         ## id and sequence are stored as key value pairs
          if ( $bow1{$ID}[1] eq $bow2{$ID}[1] ){
         #print "Identical\t$bow1{$ID}[0]\t$bow1{$ID}[1]\t$bow2{$ID}[0
+]\t$bow2{$ID}[1]\n"; #display ID and sequences  -->too many: commente
+d out
         $identical=$identical+1; #count identical pairs
         }
         else{
        print "SameID, DiffSeq\t$bow1{$ID}[0]\t$bow1{$ID}[1]\t$bow2{$I
+D}[0]\t$bow2{$ID}[1]\n"; #display ID and sequences
        $diffSeq=$diffSeq+1; #count pairs with different sequences but
+ identical IDs
        }
      }
    }
    else {
    print "Unique\t$bow1{$ID}[0]\t$bow1{$ID}[1]\t - \t - \n"; #display
+ ID and sequences
    $unique=$unique+1; #count unique IDs from first file
    }
}
$totalCount = $identical + $diffSeq + $unique; #total count - should m
+atch with total ID in first file
print "Identical\tSeq is different\tUnique in $file1\tTotal\n"; #print
+ title
print "$identical\t$diffSeq\t$unique\t$totalCount\n"; #print numbers

exit;

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In reply to UPDATE! I fixed it :D by FluffyBunny
in thread how to compare two hashes with perl? by FluffyBunny

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