Trait-based ecology characterizes individuals’ functional attributes to better understand and predict their interactions with other species and their environments. Utilizing morphological traits to describe functional groups has helped group species with similar ecological niches that are not necessarily taxonomically related. Within the deep-pelagic fishes, the Order Stomiiformes exhibits high morphological and species diversity, and many species undertake diel vertical migration (DVM). While the morphology and behavior of stomiiform fishes have been extensively studied and described through taxonomic assessments, the connection between their form and function regarding their DVM types, morphotypes, and daytime depth distributions is not well known. Here, three computer-aided morphometric techniques were used to analyze stomiiform fishes body shapes to examine the relationship between their morphology and established functional traits. Additionally, the feasibility of the three techniques to quantify preserved specimens’ shapes was assessed by measuring their ability to predict an individual's taxonomic identity. In the present study, computer-aided morphometric techniques were relatively successful in distinguishing between some taxa. Still, the extent of its success varied according to the taxa and the technique used. Functional traits associated with DVM and vertical distributions were generally significant but showed similar variability across techniques and taxa. The results of this study showed that combining computer-aided morphometric techniques with taxonomic and traditional assessments can open a wide range of new potential applications to further understand deep-sea fish morphologies and how they relate to their functioning within the deep sea. Computer-aided morphometric techniques are considered suitable methods for exploring deep-sea fish morphology variability and for a rough assessment of ecological traits within and between individuals.