Bycatch of mid-trophic level anadromous fishes that connect marine and freshwater ecosystems is a growing conservation concern. Anadromous alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) are important components of coastal freshwater and marine food webs, but have experienced dramatic declines in the abundances of spawning adults. Freshwater-focused restoration efforts have yielded few consistent signs of recovery; raising concerns that bycatch in Northwest Atlantic commercial fisheries may be negating these conservation actions. Using data from 15 microsatellites genotyped for baseline populations and bycatch, we conducted genetic stock identification to understand how bycatch was partitioned among previously identified regional genetic stocks. We then combined this information with fishery observer data to estimate genetic stock-specific bycatch mortality for the southern New England Atlantic herring fishery (2012-2013). Bycatch overall, but especially in the Atlantic herring fishery, was disproportionately assigned to the most severely depleted genetic stocks (alewife Southern New England stock – 70% of assignments; blueback herring Mid-Atlantic stock – 78% of assignments). These genetic stocks overlap in the region surrounding Long Island Sound, suggesting that bycatch taken from this area in recent years may be negatively impacting recovery efforts in this region. Our study suggests that mitigating bycatch on the southern New England fishing grounds may benefit recovery efforts for alewife and blueback herring genetic stocks that have experienced the greatest declines in spawning adult abundances.