San Clemente Island (SCI) supports one of the smallest Scripps's Murrelet (Synthliboramphus scrippsi; SCMU) colonies in the world, and perhaps the only colony of Guadalupe Murrelets (S. hypoleucus; GUMU) in California. In 2012–2016, the U.S. Navy sponsored development of a long-term murrelet monitoring program at SCI that utilized nocturnal spotlight surveys, night-lighting at-sea captures, and nest monitoring. Standardized spotlight survey transects were established in nearshore waters off breeding areas at Seal Cove and southeast SCI (SESCI). Baseline mean spotlight counts were 29 ± 15 murrelets (n = 31) at Seal Cove in 2013–2016 and 21 ± 10 murrelets (n = 15) at SESCI in 2014–2016. We banded 201 SCMU captured in congregations at Seal Cove (n = 158) and SESCI (n = 43); 12% of the SCMU from Seal Cove and 7% from SESCI were recaptured ≥1 year after banding. We also banded 21 GUMU at Seal Cove, but none were recaptured. Murrelet nests or eggs were found in 6 shoreline breeding “refuges” at Seal Cove and SESCI that were seldom if ever visited by island foxes (Urocyon littoralis clementae) and feral cats (Felis catus). Incubating SCMU were observed in 4 nest sites, but in 8 other sites only eggs or eggshells were found. Overall hatching success was very low (12%; n = 17 clutches) in 2012–2016, apparently due to intraspecific competition for limited nest crevices at Seal Cove and predation (or possibly abandonment and subsequent egg scavenging) by foxes or black rats (Rattus rattus) at SESCI. Using spotlight survey data, we estimated 115 murrelet pairs (range 79–208) at SCI, including 110 pairs (range 76–199) of SCMU and 5 pairs (range 3–9) of GUMU, although a GUMU nest has not yet been found. Power analyses of Seal Cove spotlight data indicated that surveys conducted over 9 nights per year for 20 years could reliably (power ≥ 0.90) detect minimum population changes of ±1.7% per annum. Additional efforts are needed to (1) confirm the breeding status of GUMU; (2) investigate alternative methods of rat control to increase hatching success in murrelet breeding refuges; and (3) enhance breeding habitats to reduce intraspecific competition for nest sites and increase the number of monitored nests.