We studied the male reproductive tract of individuals of different body sizes of Caecilia thompsoni to describe morphological characteristics in comparison to other Gymnophiona. The reproductive tract consists of paired testes segmented into chains of primary and secondary lobes, sperm ducts that empty to Wolffian ducts, the cloaca that receives the Wolffian ducts and possesses a phallodeum. Müllerian ducts are present and develop into paired glands that empty into the cloacal urodeum. Testicular secondary lobes contain lobules with cysts of the entire germinal cell line, whereas primary lobes, in the terminal ends of the chains, only have spermagonia, Sertoli cells, and connective tissue. The smallest individual examined (21 cm body length) was immature and only possessed a few testicular primary lobes. Once the individuals reach sexual maturity, the morphological characteristics are quite consistent at macroscopic and histological level among males of very different body sizes. The histological features of the Wolffian and Müllerian glands suggest a complementary secretory role between the two ducts. In the cloaca we found the propulsor muscle, venous sinuses, and blind sacs in the phallodeum, which differentiate C. thompsoni from other species of the genus. Despite these slight differences, the general morphological characteristics, both macroscopic and microscopic, of the reproductive tracts of adult males of C. thompsoni follow the pattern known for the reproductively active males of Gymnophiona.