Most research on ontogenetic niche shifts has focused on changes in habitat or resource use related to food resource distribution and heterospecific size-limited predation. Cannibalism, an intraspecific interaction, can also affect habitat selection or resource use by vulnerable size classes. Morphological defenses, such as spines, increase the effective size of an individual, making it more difficult to consume. The importance of such defense structures in affecting niche shifts in early life history stages is unclear. Using a combination of field observations and experiments in aquaria and wading pools, we examined the relative roles of cannibalism and morphology in determining juvenile habitat use in two populations of threespine stickleback that differ in pelvic spine morphology. Juveniles were categorized into three size classes: small (5–10 mm), medium (11–15 mm), and large (15–25 mm). In experiments assessing the relative vulnerability of juveniles to cannibalism by adults, we documented a significant difference among size classes in the number of juveniles eaten such that more large juveniles were eaten from the population lacking pelvic spines. The natural distribution of small and large juveniles in two distinct littoral microhabitats, open water and vegetation, was determined in each lake. In both populations, small juveniles were more abundant in vegetation. In the population with pelvic spines, a greater proportion of large juveniles was observed in open water than in vegetation. In the population without pelvic spines, the proportion of large juveniles did not differ between the two habitats. Experiments comparing juvenile habitat use in the presence or absence of adult conspecifics suggest that differences in habitat use may not only depend on the size of the individual, or the size of the individual relative to the size of the adult predator, but also on the degree of development or expression of defensive structures.