Microsporidian parasites of the genus Nosema, especially Nosema ceranae, continue to represent major threats to the health of Apis mellifera colonies. A promising strategy to mitigate these effects involves breeding honey bee colonies resistant to Nosema infection through molecular breeding methods such as marker-assisted selection (MAS). To enable this, it is necessary to establish reliable genetic markers for bee selection. This study aimed to investigate correlations between certain microsatellite loci and susceptibility to Nosema infection in the dark forest bee, Apis mellifera mellifera. Among the tested loci, AC117, Ap243, and SV185 were the most promising molecular markers associated with resistance to nosemosis. Their alleles “177,” “263,” and “269,” respectively, correlated with a lower infection level. This work represents the first associative investigation aimed at identifying DNA loci linked to resistance against nosemosis in dark forest bees. The discovered microsatellite markers may serve as predictive tools for estimating the likelihood of Nosema disease occurrence.