Alternative male phenotypes exist in many species and impact mating system dynamics, population genetics, and mechanisms of natural and sexual selection that operate within a population. We report on the discovery of a cryptic male phenotype in the mangrove rivulus fish (Kryptolebias marmoratus), one of only two self-fertilizing hermaphroditic vertebrates. In this androdiecious species, males are infrequent, often making up less than 5% of a population; and they have historically been described as having an orange color and lacking or having a very faded outline of the well-defined caudal eyespot (ocellus) that is obvious in hermaphrodites. The cryptic male we describe varies subtly from the hermaphrodite phenotype, without visible orange pigmentation on the body and retention or only minor fading of the ocellus. This male morph was identified by a loss of a defined melanistic "fingerprinting" on the caudal fin seen in hermaphrodites, not previously used as diagnostic for hermaphrodites, and replaced by a diffuse deposition of pigment across the fin. Individuals were identified as male with 85.7% accuracy when using these criteria. We report that in nine populations, spanning three geographically distinct regions in Florida, across two and a half years, 0.3% of the 6057 mangrove rivulus collected exhibited this cryptic male phenotype and were confirmed to have testes via dissection. Overall, 2.3% of the animals were male (normal and cryptic phenotypes), and cryptic males represented 12.9% of all males collected. Even a minor increase in individuals identified as male in a species where males make up such a small portion of the population can have important implications for population genetics. Opportunities for outbreeding are likely enhanced, which has significant evolutionary ramifications.