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The Salton Sea is a large, shallow, endorheic, polymictic, saline lake in Southern California sustained by runoff from local agricultural and municipal wastewater. As a closed-basin lake in an arid region with declining water supply, it is becoming increasingly saline. Due to its eutrophic status and episodic wind-driven mixing, basin-wide anoxia events are becoming more common during summer. Sequencing of 16S rRNA gene clones obtained from the water column and sediments provided the first molecular assessment of bacterial community structure in the Salton Sea. Similar to other saline habitats, the water column community was dominated by Gamma- and Alphaproteobacteria, and Bacteroidetes, although there was significant seasonal variability in diversity, richness, and the specific genera recovered. Sediments showed high diversity and richness and were dominated by sequences from cultured and uncultured phyla typical of marine sediments, especially the Deltaproteobacteria. This study has provided baseline data about the bacterial communities found in this important California water body and may serve as important indicators of change as the lake becomes increasingly saline over time or as remediation efforts are enacted.