The earliest stage of animal development is controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, maternal transcripts are degraded, in a tightly regulated process known as the maternal to zygotic transition (MZT). While this process has been well-studied within model species, we have little knowledge of how the pools of maternal and zygotic transcripts evolve. To characterize the evolutionary dynamics and functional constraints on the timing of early embryonic expression, we created a transcriptomic dataset for 14 Drosophila species spanning over 50 million years of evolution, at developmental stages before and after the MZT, and compared our results with a previously published Aedes aegypti developmental time course. We found deep conservation over 250 million years of a core set of genes transcribed only by the zygote. This select group is highly enriched in transcription factors that play critical roles in early development. However, we also identify a surprisingly high level of turnover of transcripts represented at both stages over the phylogeny. While mRNA levels of genes with maternally deposited transcripts are more highly conserved than zygotic genes, those maternal transcripts that are completely degraded at the MZT vary dramatically between species. We also show that hundreds of genes have different isoform usage between the maternal and zygotic genomes. Our work suggests that maternal transcript deposition and early zygotic transcription are surprisingly dynamic over evolutionary time, despite the widespread conservation of early developmental processes. Overall design: We sequenced mRNAs from individual stage 2 and stage 5 embryos (at least 3 replicates each) from 14 species. Some of the samples and species were sequenced as carrier mRNA for SliceSeq with D. melanogaster embryos (see Combs & Eisen,2013,PLOS ONE), so raw data is a mix of a small amount of D. melanogaster mRNA and mRNA from another distantly related species, as noted under samples "characteristics: raw data mixed with D. melanogaster". Other data used in the paper can be found at GSE68062 and GSE53483-renalyzed Samples, which includes stage 5 samples for D melanogaster, D. yakuba, D. virilis, and all samples from D. pseudoobscura and D. miranda.