Aberrant patches of white skin and/or fur known as hypopigmented marks, have been observed in many mammal species worldwide, but they are typically limited to only a few individuals in a population. Hypopigmented marks were documented in only two museum specimens of the federally endangered Florida bonneted bat (Eumops floridanus) as early as 1950, but recent observations suggest that these marks may be more common in this species than previously believed. To better understand the occurrence and persistence of hypopigmented marks in Florida bonneted bats, we evaluated the variation in frequency, compared effects on survival, and assessed spatial and temporal differences of specimens at an intensively studied site and across the species range. From 2014 through 2017, we regularly captured Florida bonneted bats for demographic studies at Babcock-Webb Wildlife Management Area in Charlotte County and we observed hypopigmented marks on 172 (80.8%) of 213 individuals, the highest incidence ever reported for bats. The proportion of hypopigmented marks did not differ with sex, age at first capture, or reproductive status, and importantly, we documented the persistence of hypopigmented marks in individuals over multiple months. We also found no difference in survival or capture probability between hypopigmented and solid-colored individuals. Using data from concurrent mist net studies, we assessed the proportion of Florida bonneted bats with hypopigmented marks across the species range and found a higher proportion of individuals with hypopigmented marks in the two northern counties (80.8% in Charlotte County and 61.5% in Polk County) compared to the two southern counties (21.1% in Miami-Dade County and 16.7% in Collier County). Additionally, we compared the proportion of hypopigmented individuals in Miami-Dade County between recently captured/collected bats (post-2004) and historically (pre-1965) collected museum specimens and found more hypopi gmented marks in recently captured bats. The persistence of hypopigmented marks over time, the presence of marks on bats from different locations, and our finding of no effect of age on the presence of marks all strongly suggest that the hypopigmented marks in Florida bonneted bats are the result of genetic rather than environmental factors. Further study is required to understand the mechanism underlying the high incidence of hypopigmented marks and to determine whether the prevalence of hypopigmented marks indicates low genetic diversity that could threaten Florida bonneted bats.