Motivated by data demonstrating fluctuating relative and absolute fitnesses for white- versus blue-flowered morphs of the desert annual Linanthus parryae, we present conditions under which temporally fluctuating selection and fluctuating contributions to a persistent seed bank will maintain a stable single-locus polymorphism. In L. parryae, blue flower color is determined by a single dominant allele. To disentangle the underlying diversity-maintaining mechanism from the mathematical complications associated with departures from Hardy-Weinberg genotype frequencies and dominance, we successively analyze a haploid model, a diploid model with three distinguishable genotypes, and a diploid model with complete dominance. For each model, we present conditions for the maintenance of a stable polymorphism, then use a diffusion approximation to describe the long-term fluctuations associated with these polymorphisms. Our protected polymorphism analyses show that a genotype whose arithmetic and geometric mean relative fitnesses are both less than one can persist if its relative fitness exceeds one in years that produce the most offspring. This condition is met by data from a population of L. parryae whose white morph has higher fitness (seed set) only in years of relatively heavy rain fall. The data suggest that the observed polymorphism may be explained by fluctuating selection. However, the yearly variation in flower color frequencies cannot be fully explained by our simple models, which ignore age structure and possible selection in the seed bank. We address two additional questions--one mathematical, the other biological--concerning the applicability of diffusion approximations to intense selection and the applicability of long-term predictions to datasets spanning decades for populations with long-lived seed banks.