Red sea urchins (Strongylocentrotus franciscanus), residing in shallow habitats in Bodega Bay, California are morphologically distinct and possibly enhance recruitment by spawning larvae and sheltering juveniles. This suggests shallow beds of urchins would be ideal candidates for harvest refugia promoting the production of larvae to replenish deeper harvested habitats. Red urchins from shallow beds (5 m) had significantly heavier gonads (63 ± 30 g, N = 45, mean ± 1 SD) compared with urchins from intermediate (14 m) and deep (23 m) habitats (12 ± 8 g, N = 39, mean ± 1 SD). Gonad indices from spring, summer, and fall of 1991 and 1992 show this pattern persisted. Shallow water urchins co‐occurred at high densities (4.6 individuals/m2), with seasonally abundant drift algae and wave surge. Recruitment of juvenile urchins was examined in nine 1‐m2 quadrats randomly placed in three shallow sites with red urchins and three intermediate depth sites with red urchins in the Bodega Marine Reserve. Juvenile urchin (Strongylocentrotus spp.) recruitment (5‐50 mm) was highest in association with adults in shallow habitats over a 4‐yr period (October 1988‐October 1992). Adult red urchins in shallow habitats resided in rock bowls where they were 12 times more likely to shelter juveniles than more mobile adults in deep water. Principal component analysis identified five morphological characteristics of shallow water urchins: short spines, large gonads, thick tests, small lanterns, and small peristomial openings. External morphological characteristics (e.g., spine length) could be used to ensure the protection of reproductive urchins in shallow harvest refugia offering an alternative urchin management strategy for northern California.