For ∼30 million years, the eggs of Hawaiian Drosophila were laid in ever-changing environments caused by high rates of island formation. The associated diversification of the size and developmental rate of the syncytial fly embryo would have altered morphogenic gradients, thus necessitating frequent evolutionary compensation of transcriptional responses. We investigate the consequences these radiations had on transcriptional enhancers patterning the embryo to see whether their pattern of molecular evolution is different from non-Hawaiian species. We identify and functionally assay in transgenic D. melanogaster the Neurogenic Ectoderm Enhancers from two different Hawaiian Drosophila groups: (i) the picture wing group, and (ii) the modified mouthparts group. We find that the binding sites in this set of well-characterized enhancers are footprinted by diverse microsatellite repeat (MSR) sequences. We further show that Hawaiian embryonic enhancers in general are enriched in MSR relative to both Hawaiian non-embryonic enhancers and non-Hawaiian embryonic enhancers. We propose embryonic enhancers are sensitive to Activator spacing because they often serve as assembly scaffolds for the aggregation of transcription factor activator complexes. Furthermore, as most indels are produced by microsatellite repeat slippage, enhancers from Hawaiian Drosophila lineages, which experience dynamic evolutionary pressures, would become grossly enriched in MSR content.