According to modern evolutionary biology, for understanding ontogenetic (i.e. early development) processes, it is necessary to focus on the interactions between genotype and developing phenotype, that is on both genetic and developmental epigenetic sources of information and variation. However, despite the large number of available comparative ontogenetic and eco-morphological studies on fish, there are still several studies that have so far focussed on the genotype only, in spite of advice for alternative/complementary investigations. This study bridges the knowledge gap resulting from an imbalance between studies rooted on gradual development and genetics and those based on comparative ontogeny and focussed on eco-morphology and developmental plasticity. As a case study using literature data, a new perspective is proposed on the early ontogeny of some species in the genus Hypseleotris in the light of the concept of alternative ontogenies and developmental plasticity. Based on this framework, an alternative explanation is proposed for the co-occurrence of empire gudgeon (H. compressa) and firetailed gudgeon (H. galii) in similar habitats, and for the possible existence of intraspecific twin forms within western carp gudgeon (H. klunzingeri) and of interspecific species pairs in the ‘problematic’ carp gudgeon complex (Hypseleotris spp.). Central to this paper is the model of alternative ontogenies (as opposed to the historical, descriptive approach based on ‘normal stages’ of development) and its scientific potential to provide a new reference framework for existing genetic and phylogenetic studies on problematic fish species complexes, for which only genetic studies are currently available.