Gene expression is a multi-step process that is fundamental to all cellular activities. In Drosophila oogenesis and embryogenesis both RNA localization and transcription are highly regulated and critical for proper development of the embryo. During oogenesis, maternal RNAs spatially localized within the oocyte. A few localized maternal mRNAs that are required for the proper axial patterning of the embryo have been well-studied. However, a large proportion of the genome is expressed in the ovary and deposited into the embryo. These maternally derived RNAs and proteins drive the earliest events of embryogenesis before the zygotic genome is activated and gene products derived from the zygotic genome take over the control of development. Both maternal RNA localization and early embryo gene expression have undergone substantial changes over the course of evolution in Diptera between species of different genera. However, little was previously known about the evolutionary dynamics of mRNA localization and early gene expression on shorter timescales within a genus or within a species. In this dissertation I determine the extent of natural variation in maternal and zygotic RNA complements within and between populations of a single species, Drosophila melanogaster. Additionally, I examine how maternal RNA localization changes have occurred within the Drosophila genus. In the first chapter of this dissertation, I utilize two geographically distinct populations of Drosophila melanogaster with known differences in genomic variation to examine the natural variation of maternal and zygotic transcripts within and between populations of a single species. I find that maternal gene expression has higher conservation than zygotic gene expression, similar to what has been found when comparing different species of Drosophila. Overall, there is more expression variation within populations than fixed expression differences between them. Furthermore, I find an increase in differential expression of maternal and zygotic transcriptomes within the Zambia population, a population with higher genomic variation, than the Raleigh population. I find that some of the most differentially expressed genes between populations are genes with known selection signatures corresponding to the out-of-Africa expansion of D. melanogaster. Additionally, I find an enrichment of differentially deposited mRNAs between populations on the X chromosome at stage 2, when all transcripts are a product of an XX genotype. In summary, I find that the demographic history of D.melanogaster has shaped the maternal and zygotic mRNA complements between populations of the species. In the second chapter, I present a study on differences in RNA localization along the Drosophila phylogeny. To determine the identity of localized maternal mRNAs, I bisect stage 14 oocytes from five species of Drosophila and sequenced mRNAs from the anterior and posterior halves and then performed differential expression analysis. I find several differences in localization between species. I categorize changes in localization in two categories. First, transcripts that are localized in a subset of species, while having no maternal deposition in others. This indicates lineage specific transcription as well as localization. And second, genes that are maternally deposited in all five species with enrichment to the anterior or posterior in only a subset of these species. I hypothesize that gains and losses of mRNAs could be due to new deposition of transcripts already equipped with cis-regulatory elements able to associate with localization machinery or a gene with pre-existing maternal expression that undergoes changes in regulatory elements that confer the ability to be localized. Overall, this dissertation shows that even within short evolutionary timescales there exists variation in early embryonic gene expression and mRNA localization, both critical to early development.