Lower Cook Inlet (LCI) in south-central Alaska is unusual among the breeding areas of Kittlitz's Murrelet Brachyramphus brevirostris because of human impacts on the marine and terrestrial environments and because of the lack of tidewater glaciers. In LCI the Kittlitz's Murrelet co-exists with the more abundant Marbled Murrelet, which complicates abundance estimates because of the difficulty of species identification. We compared survey data for an area with overlapping coverage in LCI (Core area) in 1993 (June) and from 1996 to 1999 (July-early August). Within this LCI Core area, the surveys in 1996-1999 estimated ~1600 Kittlitz's Murrelets and ~17 000 Marbled Murrelets, including prorated unidentified murrelets. The Kittlitz's Murrelet population declined between 1993 and 1999 at 26% per annum (84% overall). Simultaneously, Marbled Murrelets declined by 12% per annum (56% overall), though the decline was not statistically significant. Declines were estimated conservatively because the 1993 survey was conducted in June, when both murrelet species are less abundant on the water. We also surveyed Kachemak Bay, a large embayment of LCI, during mid-summer (July) of 2005-2007 and estimated a population of 2047 Kittlitz's Murrelets (SD 1120, n = 3 years) residing primarily in the inner bay. Marbled Murrelets numbered 11 040 (SD 1306) and were found throughout the bay. On one transect set in inner Kachemak Bay, Kittlitz's Murrelet density in late summer (1-16 August) declined 7.5% per annum between 1988 and 2007 (n = 6 years), and Marbled Murrelet density increased 4.9% per annum. On two other transect sets in the inner bay, however, neither murrelet species showed a change in density between 1996 and 2007. Inner Kachemak Bay is a persistent hotspot for Kittlitz's Murrelet and may attract murrelets from LCI and beyond. We recommend monitoring murrelet populations in Kachemak Bay, although Kittlitz's Murrelets likely move between the main body of Cook Inlet and Kachemak Bay, and a complete LCI survey is needed to gauge regional population trends.