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Results of electrophoretic surveys have suggested that hemoglobin polymorphism may be maintained by balancing selection in natural populations of house mice, Mus musculus. Here we report a survey of nucleotide variation in the adult globin genes of house mice from South America. We surveyed nucleotide polymorphism in two closely linked α-globin paralogs and two closely linked β-globin paralogs to test whether patterns of variation are consistent with a model of long-term balancing selection. Surprisingly high levels of nucleotide polymorphism at the two β-globin paralogs were attributable to the segregation of two highly divergent haplotypes, Hbb^s (which carries two identical β-globin paralogs) and Hbb^d (which carries two functionally divergent β-globin paralogs). Interparalog gene conversion on the Hbb^s haplotype has produced a highly unusual situation in which the two paralogs are more similar …