I’m unable to comment on this SX but I would have thought the best way to do what you wanted would have been to use a custom post type, but combine it with a custom taxonomy. In the same way that a post belongs to a category, a fish species could belong to a genus (the genus being the part defined by the custom taxonomy). The genus could then be arranged just like categories if desired – e.g. example.com/fish/apistogramma/panduro.
I’m not experienced in this area of WP development (In fact, I’m just embarking on my first project involving them at the moment) but I think they would have been a better option than modifying the slug to /genus-species.
See http://codex.wordpress.org/Taxonomies for more info.