The early development of the freshwater fish Rhytiodus microlepis is characterized by the description of external morphological, meristic, and morphometric changes, as well as the growth patterns, thereby establishing a reference for the identification of its larvae and juveniles. Specimens were collected from the Amazon river channel and floodplain. Ninety‐seven individuals were analysed with standard length varying between 4.31 and 79.23 mm. Rhytiodus microlepis larvae are altricial, with an elongated and fusiform body, anal opening reaching the middle region of the body, and simple nostrils becoming double and tubular during development. The pigments vary from one to two chromatophores in the dorsal region of the head in pre‐flexion and flexion, but later the pigmentation pattern intensifies, transverse bands appear along the body, and a conspicuous spot appears in the basal region of the caudal fin. The total number of myomeres ranges from 49 to 50. During the transition from larval (post‐flexion) to the juvenile periods, the most significant anatomical changes occur, such as the presence of all fins and increased body pigmentation. Integrated myomere count and pigmentation pattern are effective for the correct identification of the initial life stages of R. microlepis from the Amazon basin. Our results expand the knowledge about the early life history of Neotropical freshwater fish species.