The sympatric red snappers, Lutjanus erythropterus and Lutjanus malabaricus, are highly valued by commercial and recreational fishers along the tropical northern coasts of Australia and throughout their distribution. Studies on the life history and ecology of these congeners are confounded by difficulties in distinguishing the cryptic juveniles of each species (i.e., < 200 mm total length). This study aimed to validate a robust and cost-effective method to discriminate these juveniles using body and/or otolith morphometric data in a multivariate analysis. Juvenile samples were collected from the northwest (n = 71) and northeast (n = 19) coasts of Australia, and species identification was confirmed using DNA barcoding. The most parsimonious multivariate models achieved accurate species prediction rates of 98.8%, which consisted of just three body variables (dorsal fin length, the distance from the snout to the anterior edge of the eye, and either jaw length or distance from the snout to the preoperculum). The high level of discrimination for these cryptic juveniles highlights the robustness of this morphometric approach. The slightly lower rate of discrimination using otolith morphology (84.9%) was associated with greater regional variation in L. malabaricus between the northwest and northeast coasts. Slight variations in otolith shape are typically used to determine stock structure, which highlights the potential need to collect samples over a broader area of a species geographic range when using an otolith morphometric discrimination model. The method outlined in this study could be applied to distinguish other cryptic congeneric fish species, including from archived otolith collections. Moreover, this method has the potential to be utilized in assessing species compositions using body measurements from in situ stereo-video.
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