As currently defined, the Southeast Alaska (SEAK) harbor porpoise (Phocoena phocoena) stock ranges from Dixon entrance to Cape Suckling, including inland waterways. Since the early 1990s, the Marine Mammal Laboratory (MML) has conducted ship and aerial surveys to assess abundance and status of harbor porpoise in this region (Dahlheim et al., 2009; Hobbs and Waite, 2010). In recent years, analysis of ship survey sighting data from inland waters has indicated the potential for substructure within this stock. Trends in abundance between 1991 and 2012 suggested that numbers of harbor porpoise in the northern portion of the study area (Glacier Bay/Icy Strait) were stable. However, in the southern portion of the range (Wrangell and Zarembo), numbers declined significantly in the mid-2000s and subsequently increased again in early 2010 (Dahlheim et al., 2015). The decline was observed only in a region where gillnet fisheries operate. Such contrasting trends in abundance between the northern and southern portions of the range suggest the possible existence of multiple populations within the currently recognized SEAK stock. There is evidence that incidental mortality of harbor porpoise in the salmon driftnet fishery in SEAK may exceed the maximum allowable level under the Marine Mammal Protection Act (MMPA) (Muto et al., 2018). The most recent estimate of abundance for the whole stock is more than 8 years old and cannot be used to estimate PBR. In addition, estimates of abundance from inland waters from 2011 are now outdated and are no longer applicable for management. Therefore, a new estimate was needed to update estimates of the maximum allowable bycatch levels.