ABSTRACT The Pacific lamprey <em>Lampetra tridentata</em> is a native Snake River basin fish species occupying a unique ecological niche. The recent decline in numbers of returning Pacific lamprey adults to the Snake River basin has focused attention on the species. In 2000–2002, we employed electrofishing surveys to determine habitat utilization and distribution of Pacific lamprey ammocoetes in Red River, South Fork Clearwater River drainage, Idaho. Ammocoete average densities were 25.7/100 m<sup>2</sup> in scour pools, 4.4/100 m<sup>2</sup> in riffles, 2.1/100 m<sup>2</sup> in rapids, and 253.3/100 m<sup>2</sup> in the one alcove sampled. Ammocoetes were found in water depths ranging from 1.0 cm to 1.0 m; however, the two greatest densities were observed in habitat units with maximum depths greater than 0.50 m. Pacific lamprey ammocoete density decreased with increased velocity and coarse substrate, and increased with fine and medium substrates and riparian shade.