Phenotypic plasticity refers to the capacity of an organism’s phenotype to vary in response to changes in environmental conditions, without any change in the individual genotype. Sea urchins (Echinoidea) are well-known for their morphological and behavioural plasticity in response to changing habitats or trophic environments. Phenotypic plasticity has been little studied in directly developing species, in which low levels of phenotypic plasticity are usually expected as a consequence of high levels of genetic differentiation among populations and local genetic adaptation. In the present work, we report a significant plasticity in the direct-developing and brooding sub-Antarctic species Ctenocidaris (Eurocidaris) nutrix (Echinoidea, Cidaridae) through morphological and trophic analyses of gut contents and δ13C and δ15N isotopic compositions. Molecular data (COI mtDNA) confirm that the different phenotypes of C. nutrix, the short-spined C. nutrix nutrix and the long-spined C. nutrix longispina, are a single species restricted to sub-Antarctic waters. As formerly demonstrated in broadcasting echinoid species, morphological plasticity appears to be mainly linked to depth and swell exposure, specimens from exposed and shallow sites showing shorter spines and larger apical systems compared to specimens from sheltered or deep sites. Significant differences in the diet and trophic niche of the different phenotypes suggest that prey type and food diversity may also be a factor promoting distinct phenotypic responses, both in the feeding behaviour and morphology of echinoids.