A central problem in evolutionary biology is to understand how spatial and temporal variation in selection maintain genetic variation within and among populations. Brown anole lizards (Anolis sagrei) exhibit a dorsal pattern polymorphism that is expressed only in females, which occur in “diamond,”“bar,” and intermediate “diamond-bar” morphs. To understand the inheritance of this polymorphism, we conducted a captive breeding study that refuted several single-locus models and supported a two-locus mode of inheritance. To describe geographic variation in morph frequencies, we surveyed 13 populations from two major islands in The Bahamas. Morph frequencies differed substantially between major islands but were highly congruent within each island. Finally, we measured viability selection on each island to test two hypotheses regarding the maintenance of the polymorphism: (1) that spatial variation in selection maintains variation in morph frequencies between islands, and (2) that temporal variation in selection across years maintains variation within islands. Although bar females had relatively lower survival where they were rare, our data do not otherwise suggest that selection varies spatially between islands. However, diamond-bar females were subject to positive frequency-dependent selection across years, and the relative fitness of bar and diamond females alternated across years. We propose that this polymorphism is maintained by temporal variation in selection coupled with the sheltering of alleles via a two-locus inheritance pattern and sex-limited expression.