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The Gully, the largest submarine canyon off the coast of eastern Canada, is currently under consideration as a marine conservation area, primarily because of the increasing interest in oil and gas production on the Scotian Shelf. Cetaceans, as a guild of abundant, large organisms that are relatively sensitive to such threats, provide a reliable means to determine the boundaries for a conservation area in this region. We compared the abundance of cetaceans between the Gully and other parts of the Scotian Shelf and Slope and found that abundance was higher in the Gully. We also assessed cetacean distribution and relative abundance within the Gully relative to search effort for several spatial and temporal parameters: depth, slope, sea surface temperature, and month. Distribution within the Gully was most strongly correlated with depth, but was also significantly correlated with sea surface temperature and month. Five of the 11 cetacean species commonly found in the Gully, and all those for which the Gully formed significant habitat on the Scotian Shelf, were concentrated in the deep (200–2000 m) mouth of the canyon. We suggest that a year‐round marine protected area is necessary for the Gully. A core protection zone should be defined in the Gully based on depth and bounded by the 200‐m isobath. A buffer zone around the core zone should be defined to provide protection from activities with further‐reaching effects, such as noise, dredging, and chemical pollution.

The use of natural marks in capture‐recapture studies can lead to unequal capture probabilities. This paper examined a catalog of northern bottlenose whale (Hyperoodon ampullatus) photographs from the Gully, Nova Scotia, to identify potential sources of heterogeneity. This information can be used to select appropriate individuals and photographs to include in analyses. Individual northern bottlenose whales were sufficiently marked to uniquely identify individuals (x̄= 14.5 marks/individual; range 1‐67), but not all mark types persisted over time. Reliable marks were defined as mark types that were not lost over the nine‐yeat study period (notches, back indentation, and mottled patches). Individuals were considered reliably marked if they possessed at least one back indentation or mottled patch (located within one dorsal fin width, at the base of the dorsal fin) or a notch on the dorsal fin. Sixty‐six percent (SE = 5%) of the population were reliably marked. Longterm analyses (months to years) should use only reliably marked individuals, and the results scaled to account for the rest of the population. Our results also showed that photographic quality affected an observer's ability to identify individuals. For this catalog, quantitative analysis indicated only photographs of Q ≥ 4 (on a 6‐point scale with 6 representing the highest quality) should be included in mark‐recapture analyses sensitive to heterogeneity.

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