Cichlid fishes are an ideal model system for studying diversification because they provide textbook examples of extremely rapid evolution and speciation through adaptive radiation. Although gene regulation has been widely recognized to be an important mechanism that links diversification in gene function to speciation, so far its role in cichlid speciation has received little attention. We investigated the potential importance of miRNA regulation in the diversification of six cichlid species of the Midas cichlid adaptive radiation (Amphilophus spp.) from Nicaraguan lakes. Using several genomic resources we discovered 236 Midas miRNA genes that were then used to predict miRNA target sites in 8,232 Midas 3’ UTRs. Using population genomic calculations of SNP diversity we found miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlids, but similar to what is typically found in other organisms, we observed genomic signatures of purifying selection on miRNA targets by comparing these sites with less conserved non-target portions of the 3’ UTRs. Interestingly, in one species pair that putatively speciated sympatrically in crater Lake Apoyo, we found a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites might be an important mechanism that contributes to the rapid phenotypic evolution of the Midas cichlid adaptive radiation from Nicaragua, but also in cichlid fishes more generally.