Hello Pasan and welcome to the Monastery.

Of course your code will print "match found" because that is what you are telling it to do. Dump the content of $fastaH1 through Data::Dumper to see how your hash looks like. My piece of advice is that if you are reading from a Bio::SeqIO object then you got to write your output through a Bio::SeqIO object as well. That way you will save yourself from a lot of the unexpected Bio::* behaviors.

other things I noticed in your code is that your open statement doesn't capture failure. Alsoe, if you're using a Bio::SeqIO then you don't need to explicitly import all the parent modules.

use strict;    #a good habit to start your prog
use warnings;
use Bio::SeqIO;

#load your codes.txt into an array
open(my $fh, "<","codes.txt") or die("could not open codes.txt $!"); #
+a more proper way to opening files

my @codes=<$fh>;    #slurping codes.txt into an array

my $obj=Bio::SeqIO->new(     #Bio::SeqIO for input
    -file=>"fasta.fa",
    -format=>"fasta"
    );

my $out_obj=Bio::SeqIO->new(  #Bio::SeqIO for output
    -file=>">matching.fa",
    -format=>"fasta"
    );
while(my $seq=$obj->next_seq){
    foreach my $element (@codes){
        chomp $element;
        if($seq->id=~/$element*?/gi){    #regular-expression based mat
+ching 
            $out_obj->write_seq($seq); #output written to matching.fa
            }
        }
    }
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