Acoustic surveys were conducted in late summer/early fall during the years 1992-1996 and 2001-2012 to estimate pelagic prey fish biomass in Lake Michigan. Midwater trawling during the surveys as well as target strength provided a measure of species and size composition of the fish community for use in scaling acoustic data and providing species-specific abundance estimates. The 2012 survey consisted of 26 acoustic transects (576 km total) and 31 midwater tows. Mean total prey fish biomass was 6.4 kg/ha (relative standard error, RSE = 15%) or 31 kilotonnes (kt = 1,000 metric tons), which was 1.5 times the estimate for 2011 and 22% of the long-term mean. The increase from 2011 resulted from increased biomass of age-0 alewife, age-1 or older alewife, and large bloater. The abundance of the 2012 alewife year class was similar to the average, and this year-class contributed 35% of total alewife biomass (4.9 kg/ha, RSE = 17%), while the 2010 alewife year-class contributed 58%. The 2010 year class made up 89% of age-1 or older alewife biomass. In 2012, alewife comprised 77% of total prey fish biomass, while rainbow smelt and bloater were 4 and 19% of total biomass, respectively. Rainbow smelt biomass in 2012 (0.25 kg/ha, RSE = 17%) was 40% of the rainbow smelt biomass in 2011 and 5% of the long term mean. Bloater biomass was much lower (1.2 kg/ha, RSE = 12%) than in the 1990s, and mean density of small bloater in 2012 (191 fish/ha, RSE = 24%) was lower than peak values observed in 2007-2009. In 2012, pelagic prey fish biomass in Lake Michigan was similar to Lake Superior and Lake Huron. Prey fish biomass remained well below the Fish Community Objectives target of 500-800 kt, and key native species remain absent or rare.