Coral snakes have restricted and specialized diets, and their semifossorial and aquatic habits make them difficult to observe or collect. As a consequence, there is limited information about many aspects of their biology, including genetic diversity. Microsatellite markers have been used to study genetic variability in nonmodel species, such as snakes. The aim of this work was to develop primers for microsatellite regions of the genome of Micrurus surinamensis, to test transferability potential to Micrurus lemniscatus and Micrurus paraensis, and to analyze the genetic diversity of those species. DNA of one specimen of M. surinamensis was sequenced on the MiSeq platform, and sequences were searched for microsatellite regions with 10 primers designed for regions having tetranucleotide motifs. Micrurus surinamensis (n = 12 individuals) presented from 5 to 13 alleles and expected heterozygosity ranged from 0.741 to 0.939. Eight markers were successfully transferred to M. lemniscatus (n = 38) and five to M. paraensis (n = 13). The probability of exclusion of paternity ranged from 0.997 to 0.999 for species, and the probability of combined identity was lower in M. surinamensis (8.41 × 10−9). These are the first microsatellite markers to be used for studies of coral snake population genetics and conservation.