Formalinized specimens used in mitochondrial DNA (mtDNA) studies have shown shortcomings with respect to efficacy of DNA isolation and subsequent PCR amplification. In order to pinpoint the source of some of the problems with formalinized tissues in reptiles, we compared the efficacy of isolation and amplification of mtDNA from two different snake species Micrurus fulvius and Lampropeltis triangulum—that differ in composition of tissues typically sampled (intercostal muscle tissue) by researchers performing mtDNA analyses in snakes and other reptiles. This study shows clearly that the more muscle-fiber rich L. triangulum tissues yield higher quality mtDNA that is easier to manipulate with PCR than the myocyte depauperate Micrurus tissues. We suggest that curatorial practice in making available formalin preserved specimens in reptiles should focus on tissue type, most appropriately on muscle-rich tissues. We reiterate previous caution about minimizing amplicon size and maximizing controls for contamination when working with formalin-preserved reptile tissues.