The determination of embryonic stages is very useful in comparative and evolutionary anatomy, experimental research and ecological studies. Although tables of development stages already exist for some crocodilian species, no table has yet been published for Melanosuchus niger. Therefore, the aim of this work is to monitor the development of this species of Alligatoridae and characterize its stages based on the main morphological transformations the embryo undergoes during the incubation process. Under natural conditions, two samples were collected daily in the Lake Cuniã Extractive Reserve in Rondônia, Brazil, making a total of 186 eggs. The incubation period was 90 days at an ambient temperature varying from 25.2 to 31.7 °C. We established 24 embryonic stages between the formation of the pharyngeal arch and hatching. Primordia for the sensory organs and somites were observed in the early stages. The buds of the pelvic and thoracic limbs emerged simultaneously, also in the early stages. An analysis of these structures showed evidence of considerable evolutionary modifications when compared with embryos of different species. In stage 12 we observed subtle pigmentation in the region of the head and, in stage 25, the pigmentation and striped pattern were typical of the newly hatched specimen. The eyetooth was visible in stage 18, disappearing within the first few weeks after hatching. The vitellus was completely absorbed in the penultimate stage. Direct comparisons of the table of embryonic stages were made between M. niger and other crocodilian taxa, and the main differences identified were chronological variations.