Urbanization impacts wildlife, yet research has been limited to few taxa. American alligators (Alligator mississippiensis) are apex predators that have received minimal attention within urban areas. We investigated potential effects of urban land use on alligators through surveys of relative alligator abundance in nine tributaries of the lower St. Johns River within Jacksonville, FL. We then explored the potential effects of urban development on alligator spatial distribution and habitat selection at coarse and fine scales. At the coarse scale, we found no correlation between percent developed land and alligator abundance across tributaries; instead, salinity was the primary driver. However, at the fine scale alligators preferred habitats with more open water and vegetated shorelines and avoided anthropogenic structure. Surprisingly, only one of 93 sighted individuals was an adult. Hunting and nuisance alligator data suggests that adults are relatively rare in Jacksonville because they have been targeted for removal. Thus, smaller alligators still occupy urban habitats because they are not targeted and face no competition from adults. Increasing urbanization and human activity may further degrade alligator habitats and limit the distribution of breeding adults, potentially leading to local population declines.