#!/usr/bin/perl

use strict;
use warnings;

my $word1 = 'Hcr1fa.fa'; # you missed the ;

if ( $word1 eq "chr1.subst.fa" ){ # I added quotes
	print "$word1\n"; 
} elsif ( $word1 eq "Hcr1fa.fa" ) { 
	print "$word1\n" 
}