Focal species are a critical component of conservation planning, along with representation of ecosystems, special elements and ecologically sustainable management. They warrant conservation attention because they are functionally important, wide-ranging or space-demanding, habitat-quality indicators, ‘flagship’, and/or vulnerable or special populations. A delphi survey matrix-based approach, involving regional experts in the selection of potential focal species, was applied in Nova Scotia, Canada and Maine, USA. Matrices with native species on one axis and selection characteristics on the other axis were used to summarize expert knowledge and judgment. Characteristics were related to biological traits and habitat requirements that make some species more vulnerable than others in human-modified landscapes. In Nova Scotia and Maine, 19 and 11 experts, respectively, completed the matrices, which were subsequently numerically assessed. Species with the highest scores were identified as potential focal species, including wolf, cougar, lynx, river otter, eastern pipistrelle, wood turtle, four-toed salamander, golden eagle and Atlantic salmon. Concerns remain around the lack of representation of some classes of species, subjectivity in selecting and weighting characteristics, and the relative nature of assessing species against the characteristics. Accordingly, potential focal species should be subject to verification through more rigorous and quantitative analysis and monitoring. Nonetheless, if applied with care, the matrix-based approach can provide a relatively systematic and effective way of engaging regional experts in focal species selection.