The Monks above are all correct that using require or use if will allow you to load the module at runtime based on your conditional. But I think this is a perfect place for taking advantage of one of the most powerful OO features, polymorphism.

use Human;
use Mouse;

my %classes = ( H => 'Human', M => 'Mouse' );
my $species = get_species();      # returns 'H' or 'M'
my $organism = $classes{$species}->new;
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This will allow you to instantiate a different object depending on whatever is returned by the get_species function. For more, take a look at perltoot.