Identifying the developmental and molecular architecture of adaptation is a key goal of evolutionary geneticists. In this study, we focus on transcriptome differences in two selection treatments in Drosophila melanogaster, “Fast” and “Slow”, which have been selected for extreme developmental timing phenotypes for over 1000 generations with controlled replication. These selection treatments differ in life cycle length, with “Fast” flies having a shortened life-cycle of 9 days and “Slow” flies having an extended life-cycle of 28 days, from egg laying. We assessed the duration of developmental transitions by assessing larval and pupal morphology every two hours for 6 days. Remarkably, we observe highly concordant phenotypic adaptations among independently evolved populations, suggesting the existence of a limited set of developmental pathways involved, consistent with convergent molecular evolution. The developmental stage most impacted by the selection treatment is transition to 3rd instar larvae, which shows an average reduction of ~20 hours (~35%). To determine the molecular basis for these phenotypes we performed RNA-Seq on diverse stages of both Fast and Slow development. Enrichment for body morphogenesis-related pathways and strong conservation of gene expression changes among independently evolved biological replicates corroborated our observations. Together these findings suggest that divergent selection produces differences in gene regulation that are not necessarily mirrored by differences in the selected phenotype. We are further dissecting the contributions of cis and trans gene expression adaptations by mapping allele specific expression in Slow/Fast hybrids.