The Little River is a highly disturbed system, heavily impacted by non-point source pollution from agricultural runoff in the form of excessive siltation, nitrogen and phosphorus, and organic pollution. Sixty-seven taxa of non-diatom benthic algae were documented for 16 sites in the Little River basin of western Kentucky during four sampling periods in 2000 and 2003. Algal taxa most often encountered included members of the Cyanophyta: Oscillatoria lutea (15 of 16 sites), O. subbrevis (13 of 16 sites), and Schizothrix calcicola (15 of 16 sites). Chlorophyta taxa most often encountered included Oedogonium sp. and Rhizoclonium hieroglyphicum, both at 10 of 16 sites. No trends were found between the algal taxa and areas of nutrient enrichment in the Little River basin. Because little is known of the benthic algal flora in the Little River, this report represents information complementary to that published previously on the benthic diatom taxa found at the same sites during the same study period.