Transcriptional regulation plays a central role in executing a developmental program. On the other hand, changes in gene regulatory networks are considered as important drivers of the diversity of developmental programs. Our aim is to study conserved and divergent interactions in the gene regulatory network (GRN) underlying photoreceptor specification, downstream of the retinal determination network operated by toy, ey, so, eya, dac. To this end we performed a comparative genome-wide expression study in eye-antennal and wing imaginal discs across three Drosophila species, namely D. melanogaster, D. yakuba, and D. virilis, using Tag-Seq profiling. We first solved issues of incomplete genome annotation in D. yakuba and D. virilis and optimized the preprocessing and normalization. Next, we integrated the expression ratios of the three species with order statistics and identified a highly conserved core of eye-specific genes. Using cis-regulatory sequence analysis we identified Glass as a key regulator of this conserved gene signature. Particularly, the tool CisTargetX finds the Glass position weight matrix (PWM) as the highest ranked motif within a library of 3731 PWMs, and yields 32 conserved direct Glass targets. We validated our predictions by qRTPCR in four different glass mutants and confirmed around 70% as true positive glass targets. We are currently investigating evolutionary changes of the glass targetome, both at the level of the GRN and at the level of the cis-regulatory modules.