my %ids;

$origsql = qq{ SELECT route_number, stop_reference, depart_time FROM routes WHERE distance < 200...........}; #all SQL code not included here
$sth = $dbh->prepare( $origsql );
$sth->execute();
$sth->bind_columns( undef, \$orig_service_id, \$orig_stop, $depart_orig);
while ($sth->fetch())
{
push(@orig_service_ids, $orig_service_id);
}
for my $id (@orig_service_ids) {
    $ids{$id} = 1;
}

# ...


$destsql = qq{ SELECT route_number, stop_reference, depart_time FROM routes WHERE distance < 200...........}; #all SQL code not included here
$sth = $dbh->prepare( $destsql );
$sth->execute();
$sth->bind_columns( undef, \$dest_service_id, \$dest_stop, $depart_dest);
while ($sth->fetch())
{
push(@dest_service_ids, $dest_service_id);
}
for my $id (@dest_service_ids) {
    if (exists $ids{$id}) {
        print "ID $id exists in both origin and destination set\n";
    }
}