Welcome to the Monastery and welcome to Perl!

The first error you are probably getting is from this line:

my $outfile = "$accession_$biotype";
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The dollar sign signifies a variable name, and the double quotes are trying to interpolate a variable which you have not declared yet with my. If you really want an output file named $accession_$biotype with literal dollar sign characters in it, you could try using single quotes to prevent interpolation, and hence, to make Perl understand that it is just a string, not a variable name:

my $outfile = '$accession_$biotype';
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But, what I really think you are trying to do is to keep opening a new output file with a different name. In that case, somewhere inside your loops, you would:

$outfile = "${accession}_${biotype}";
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or, equivalently:

$outfile = $accession . '_' . $biotype;
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Update: maybe you are looking for something close to this UNTESTED code:

use strict;
use warnings;

my $genfile = "c:\bemisia_coi.gb";
my $outfile;
my ($OUT, $IN);

print "Input: $genfile\n";
open $IN, '<', $genfile or die "cannot open $genfile: $!\n";

while (<$IN>) {
   $_ = lc $_; #case insensitive
   my @tokens = split m{//};
   for my $token (@tokens) {
         my ($accession) = ($token =~ /locus\s*([a-z]{8})/);
         my ($biotype)   = ($token =~ /biotype: ([a-z]{1})/);
         my ($sequence)  = ($token =~ /origin(\*+)\/\//);
            $sequence =~ s/\s//g; #Removing spaces
            $sequence =~ s/\d//g; #Removing numbers

        $outfile = "${accession}_${biotype}";
        open $OUT, '>' $outfile or die "cannot open $outfile: $!\n";
        print "Printing to $outfile \n";
        print $OUT, ">$outfile/n^^/n$sequence");
   }
}
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