When faced with the daunting and exciting task of studying biodiversity, one must necessarily come to terms with a few challenging knowledge gaps, the so‐called biodiversity shortfalls. Given that biodiversity is inherently multidimensional, it seems rather natural to admit that hitherto unrecognized shortfalls, on other distinct aspects of biodiversity, should be considered. Here, we introduce the Haeckelian shortfall, which has as its nexus organismal ontogeny, and refers to the relative scarcity of knowledge about the distinct semaphoronts of a substantial fraction of all known species. The Haeckelian shortfall has a profound relevance on the matter of total evidence, in the context of systematics, besides several indirect effects on the other shortfalls, as they all are intimately interconnected. The importance of studying distinct semaphoronts is crystal clear: Besides the purest and most descriptive access to the ontogeny of species (the idiographic aspect), assessing those semaphoronts will certainly promote the advancement of relevant nomothetic knowledge, contributing to an increasingly meaningful eco–evo–devo. Overcoming the Haeckelian shortfall is certainly a major challenge in our task of knowing and preserving biodiversity.