The practice of modern evolutionary and ecological research is interdisciplinary, with the process of evolution underpinning the diversity on display. However, the inference of evolutionary patterns can be difficult owing to their historical nature. When the biological units and evolutionary relationships involved are unclear, interpreting any ecological and biological data can be problematic. Herein we explore resulting issues when evolutionary theories rely on an unclear or incomplete biological framework, using some Australian freshwater fish (carp gudgeons: Hypseleotris, Eleotridae) as an example. Specifically, recent theories regarding the role of developmental plasticity on ontogeny and speciation have focused on this group. However, carp gudgeons have complex, and as yet incompletely understood, species boundaries and reproductive biology. Even basic data for the recognised taxa, relating to their phylogenetic relationships, life histories and species distributions, are unclear, have often been misinterpreted and are still in the process of being assembled. Combined, these factors make carp gudgeons a relatively poor group on which to apply more advanced evolutionary theories at the moment, such as the role of developmental plasticity in diversification.