Cichlid fishes are among the most diverse and speciose vertebrate clades. Their bright mating colors are matched by equally diverse visual sensitivities. Species vary in the wavelengths of light they detect and that variation can drive cichlid speciation. Cichlid visual sensitivities arise from the expression of different subsets of seven cone opsin genes. We are using genomic approaches to characterize the gene regulatory networks controlling opsin expression in Lake Malawi cichlids. At least 6 QTL affecting opsin gene expression have been identified in multiple F2 crosses between species with varying expression. One of these QTL is a putative cis regulatory locus located in or near the SWS1 opsin gene. The other QTL are not near opsin genes, and represent trans-acting loci. Using network analysis of retinal transcriptomes and association mapping across species, we have identified transcription factors in several of these QTL that control expression of the SWS2A (blue sensitive) and LWS (red sensitive) opsins. Insertions and deletions in the cis-regulatory regions of these transcription factors are highly correlated with opsin expression. The transcription factors are on different chromosomes so that opsin expression is not correlated in F2 progeny. However, expression is correlated among species, suggesting that particular combinations of opsins might be optimal and so selected. Further, these indels are sorting through the entire Malawi flock and are likely ancestral polymorphisms within the lake. These causative loci suggest a role for ancestral insertion/deletion polymorphisms in creating cichlid diversity.