Basic information on species distribution and abundance is often lacking, even for common species. The historically abundant Mountain Yellow-legged (Rana sp.) and Pacific Treefrog (Pseudacris sp.) species complexes occur sympatrically and are exposed to similar threats. We evaluated the status of these species complexes on national forest lands in the Sierra Nevada, California as part of a long-term bioregional amphibian monitoring program. To determine occupancy and abundance indices, we surveyed all lentic and a sample of lotic habitats in 208 small watersheds (2–4 km²) selected using an unequal probability design where watersheds occupied previously had a higher likelihood of being selected. For Rana sp., results corroborated other assessments that the taxon has declined substantially. We found breeding activity in an estimated 0.04 (SE = 0.01) of watersheds rangewide, 0.47 (SE = 0.04) of watersheds with locality data from 1990–2001, and 0.02 (SE = 0.03) of watersheds with locality data prior to 1990. Less than 10% of the watersheds contained large numbers of frogs (>500 tadpoles or 100 adults subadults). In contrast, treefrogs were still distributed widely, with breeding occurring in an estimated 0.25 (SE = 0.01) of watersheds rangewide and 0.95 (SE = 0.02) of watersheds where the taxon was assumed to have occurred historically. The status of Rana sp. is consistent with broad-scale predictions that highly aquatic, specialized anuran species have an increased extinction risk. The delayed recognition of the severity of Rana sp. declines underscores the value of an early warning monitoring system for all species including common ones.