There are currently no quantitative studies describing the habitat of Desmognathus organi (Northern Pygmy Salamander) and D. wrighti (Southern Pygmy Salamander). We investigated the relative abundance and microhabitat selection of Northern Pygmy Salamander and Southern Pygmy Salamander in 3 forest types of different elevations across the mountains of North Carolina during the summer of 2015. We conducted 2-h time-constrained searches at 4 sites in Picea rubens (Red Spruce) —Abies fraseri (Fraser Fir) forests, northern hardwood forests, and mountain cove forests for each species. We quantified microhabitat characteristics at each pygmy salamander location and at a corresponding random location 2–30 m away. We captured a total of 98 pygmy salamanders (D. organi = 41, D. wrighti = 57): 52 in spruce—fir forests, 26 in northern hardwood forests, and 20 in cove forests, and recorded 655 other salamanders representing 15 species. Relative abundance of pygmy salamanders was greater in spruce—fir forests than in cove forests, but was not significantly different between spruce—fir and northern hardwood forests. Microhabitat did not differ between Northern Pygmy Salamander and Southern Pygmy Salamander for any of the variables examined, except for soil moisture, which was greater at Northern Pygmy Salamander locations and may have been a spurious result. We observed pygmy salamanders almost exclusively beneath wood cover-objects, and size of cover objects did not differ from the size available in the surrounding environments. Total area of small-sized down woody debris (DWD) and total area of large-sized DWD were the only variables associated with the presence of pygmy salamanders, suggesting that pygmy salamanders avoid predation and interspecific competition by selecting sites that minimize encounters with larger salamanders.