A proper understanding of tissue and cell structure is of great importance for correct biological inferences, and particularly so in organisms used as research models. Nothobranchius spp. are short-lived freshwater fish species which are promising model organisms for toxicology, evolutionary ecology, aging and regeneration research. Nevertheless, studies examining Nothobranchius histology have focused exclusively on a few specific organs and associated functional impairments, and there is a lack of reference material on the natural state and appearance of tissue structure. Here we present a detailed histological map of the major body organ systems, which was built from 300 Nothobranchius spp. specimens. This overview offers baseline material for comparative histological studies and provides insights into functional and anatomical aspects of organs related to the unique life cycle of Nothobranchius spp.