Copepods are crustacean zooplankton that collectively form one of the most abundant groups of animals on Earth. In the polar oceans, some copepods store large amounts of lipids, making them a critical food resource for higher trophic levels. In this study, we focus on two dominant Southern Ocean copepods that differ in the chemical makeup of their lipid stores. Calanoides acutus is predominantly herbivorous and primarily stores wax esters, while Calanus propinquus is more omnivorous and stores triglycerides. Adult females of both species were subject to a shipboard experiment, where they were either fed or starved for 9 days and characterized with RNA-seq. We use these experimental data in conjunction with a phylogenetic gene family-level approach to compare the transcriptomic starvation responses of these species. At a broad level, starved individuals of both species downregulate genes related to lipid metabolism and transport, including hydrolases and lipases that catalyze steps in lipid degradation. By explicitly considering the homologous relationships between genes, we test whether, and to what extent, the starvation response is mediated by the same orthologs and gene families. We characterize a conserved starvation response, which may be shared among diverse pelagic copepods, as well as differences in gene expression underlying the two divergent modes of lipid storage.