We used blood samples from 175 individuals of the Australian lizard Egernia stokesii to determine infection status of three apicomplexan blood parasites from the genera Hemolivia, Schellackia, and Plasmodium and to determine genotypes at 12 microsatellite DNA loci. We found one significant association between genotype and infection status. For locus Est4, individuals carrying allele 159 had lower prevalence of infection with Hemolivia (14.3% of 28 lizards) than individuals that did not carry the allele (58.4% of 89 lizards). We interpret this as a linkage to a functional gene associated with parasite resistance. We found no evidence among seven lizard populations that the frequency of allele 159 was related to the population prevalence of Hemolivia infection and discuss several explanations of that pattern.