If you want to accumulate all your data into one hash, you need to declare it outside the while loop:

use warnings;
use strict;
use Data::Dumper;

my %genus;
while ( my $line = <DATA> ) {
    chomp $line;
    next if $line =~ /Query=/;
    my @hit = split( /\s/, $line );
    $genus{ $hit[2] }++;
}

print Dumper(\%genus);

__DATA__
Query= 16sV5:44:FC62N5DAAXX:7:1:18808:1248 1:N:0:
1111599 AB563244.1 Streptococcus macedonicus str. W28                
1111215 AB563262.1 Streptococcus equinus str. MTS6
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prints...

$VAR1 = {
          'Streptococcus' => 2
        };
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