We sampled with acoustics (AC) and midwater trawls (MT) to determine cisco abundance in Lake Superior’s Thunder and Black bays during 8-14 November, 2009. Total abundance of spawning-size (≥ 250 mm total length) ciscoes was estimated at 6.25 million in Thunder Bay and 1.12 million in Black Bay. Exploitation fractions of market-size (≥ age 6) females from Thunder and Black bays for 2009 were estimated at 7.1% and 11.3%, respectively; below the recommended maximum annual harvest of 15% recently adopted by Lake Superior fisheries managers. Given Thunder Bay spawner densities are on a downward trajectory, and recruitment since the 2003 year-class has been low, it is likely the exploitation fractions will increase in the future. After 2010, the Ontario Ministry of Natural Resources (OMNR) will carry on the AC program as a management activity. It is likely suspended experimental gill net (GN) samples will be used to ground truth future AC samples. In 2009, we characterized the length and age structure of Thunder Bay ciscoes using both MT samples and GN samples. Females represented 49% of the MT catch, but only 39% in GN samples. Catching a smaller proportion of females in GN samples resulted in a lower female population estimate and a higher estimated exploitation fraction (10.4%) compared to MT samples (7.1%). Experimental gill net effort was limited to 10-11.8 m water column depths where midwater trawl samples also caught roughly 40% females. Ciscoes ≥ age 17 (≥ 1992 year class) were common in Black Bay, but rare in Thunder Bay suggesting: 1) the stocks may be distinct; and 2) total mortality of ciscoes returning to spawn in Black Bay in recent years has been lower than ciscoes returning to Thunder Bay. Our mid-November 2009 effort to assess the Black Bay stock by sampling outside of the 3 bay in the lake proper was deemed successful, but this should be confirmed by sampling the Black Bay region during both mid- and late-November 2010.