Shifts in behaviors and morphology are often hypothesized to be involved in an organism’s transition to a novel ecological niche, but the relative importance of each of these changes is still unknown. Here, we use a young adaptive radiation of Cyprinodon pupfishes to investigate which phenotypic shifts are necessary to occupy the ecological niches of scale- and snail-eating. There are currently several hypothesized origins for scale- and snail-eating that include shifts in: aggression, feeding kinematics and preference, mate preference, and craniofacial morphology. We investigate each of these hypotheses using behavioral and kinematic assays, transcriptomic data, and quantitative trait locus mapping. We found increased levels of aggression in both scale- and snail-eaters compared to generalists, suggesting that increased aggression is important to the occupation of both niches. Shifts in feeding behaviors were also important for both scale- and snail-feeding performance but shifts in morphology (i.e. larger jaws) increased scale-eating performance, while snail-eating performance was independent of the morphological shifts observed in the species (i.e. increased nasal protrusion size). Furthermore, generalist and snail-eating pupfish exhibited strong mating biases against scale-eating mates, suggesting that pre-mating isolation plays a larger role in occupation of the scale-eating niche. Ultimately, we conclude that shifts in behaviors such as aggression and feeding preference/kinematics may be universally important for colonizing a new ecological niche, but that additional shifts in morphology or pre-mating isolation are needed to occupy a truly novel niche such as scale-eating.