Many bivalves have an unusual mechanism of mitochondrial DNA (mtDNA) inheritance called doubly uniparental inheritance (DUI) in which distinctly different genomes are inherited through the female (F genome) and male (M genome) lineages. In fertilized eggs that will develop into male embryos, the sperm mitochondria remain in an aggregation, which is believed to be delivered to the primordial germ cells and passed to the next generation through the sperm. In fertilized eggs that will develop into female embryos, the sperm mitochondria are dispersed throughout the developing embryo and make little if any contribution to the next generation. The frequency of embryos with the aggregated or dispersed mitochondrial type varies among females. Previous models of DUI have predicted that maternal nuclear factors cause molecular differences among unfertilized eggs from females producing embryos with predominantly dispersed or aggregated mitochondria. We test this hypothesis using females of each of the two types from a natural population. We have found small, yet detectable, differences of the predicted type at the proteome level. We also provide evidence that eggs of females giving the dispersed pattern have consistently lower expression for different proteasome subunits than eggs of females giving the aggregated pattern. These results, combined with those of an earlier study in which we used hatchery lines of Mytilus, and with a transcriptomic study in a clam that has the DUI system of mtDNA transmission, reinforce the hypothesis that the ubiquitinproteasome system plays a key role in the mechanism of DUI and sex determination in bivalves. We also report that eggs of females giving the dispersed pattern have higher expression for arginine kinase and enolase, enzymes involved in energy production, whereas ferritin, which is involved in iron homeostasis, has lower expression. We discuss these results in the context of genetic models for DUI and suggest experimental methods for further understanding the role of these proteins in DUI. Proteomics has made a rapid progress when applied to model species where genomic databases are well developed, but recent reviews have pointed to the growing interest in applying proteomics to nonmodel species in areas such as evolutionary ecology (1), aquatic toxicology (2), aquatic pollution (3), aquaculture (4), and marine biology (5). In the marine mussel genus Mytilus, an unusual system of mtDNA inheritance occurs characterized by the presence of two mitochondrial genomes (called F and M) one of which is inherited maternally and the other paternally (6 -9). This phenomenon, called doubly uniparental inheritance of mtDNA (DUI), 1 suggests a connection between mtDNA inheritance and sex determination. DUI also occurs in other species belonging to three bivalve orders (10, 11). Since the 1990s, DUI has been under intensive investigation, but the molecular mechanism for DUI and how it relates to sex determination, is still to be elucidated (for review, see 12-15).Cytological studies of fertilize...