Mammalian skeletal muscle and the homologous Drosophila melanogaster somatic muscle are composed of large cells called myofibers, each containing many muscle nuclei or myonuclei. These larval somatic muscles follow a precise and highly stereotyped pattern in their position, orientation, size and number of nuclei laid down in early development. Over the course of larval development, the somatic muscles then undergo extraordinary changes as they grow many fold in size and DNA content, all while maintaining their spatial patterning. However, the extent to which myonuclear transcription is itself patterned, within the larval somatic muscles of Drosophila melanogaster as well as during development where transcriptional differences between myonuclei emerge, are not well understood. In this thesis, we sequenced RNA from Drosophila melanogaster larval nuclei at two timepoints during third instar larval development. The goal was to characterize the spatial and temporal patterning of the somatic myonuclei during this critical developmental stage. We then validated the positioning and developmental timing of these myonuclear populations using fluorescence in-situ hybridization against cluster markers. We identified three populations of larval myonuclei: the first was Generic myonuclei, analogous to mammalian ‘body’ myonuclei. The second was Retained+ myonuclei, which consisted primarily of myonuclei in the anterior larval somatic muscles. These Retained+ myonuclei were present on both days of third instar larval development and, we suggest, are responsible for maintaining muscle homeostasis within the highly active anterior muscles. The third was the Tolkin+ myonuclei, which consisted primarily of myonuclei in the posterior larval somatic muscles. These Tolkin+ myonuclei emerged during the second (and final) day of third instar larval development. We suggest that the emergence of this cluster is responsible for priming the larval muscles for histolysis or programmed cell death at the end of larval development and formation of the prepupa. In contrast to murine sequencing studies, our analysis found neither evidence of subpopulations of NMJ or MTJ myonuclei nor that the populations present had meaningful differences in intracellular position. These results show that myonuclear transcription in Drosophila melanogaster larval somatic muscle during this stage of development is organized by organismal patterning, both spatially along the anterior-posterior axis and temporally.