Cryptic species (evolutionarily distinct lineages that do not align with morphologically defined species) are being increasingly discovered but are poorly integrated into ecological theory. In particular, we still lack a useful understanding of if and how cryptic species differ in ways that affect community recovery from disturbances and responses to anthropogenic stressors, such as the removal of consumers and pollution from nutrients. On coral reefs, nutrient pollution increases the growth of macroalgae that displace corals. Reductions in herbivorous fishes reduce the suppression of macroalgae, while reductions in coralivorous fishes reduce predation on corals. An unresolved question is if and how cryptic coral species respond differently to these impacts, thereby differing in their ability to influence coral community dynamics and maintain coral dominance. Therefore, we assessed how the response of cryptic Pocillopora species over a period of three years following a simulated disturbance from a cyclone depended on the experimental reduction of fish consumer pressure and nutrient addition. After three years, five morphologically cryptic, but genetically distinct, Pocillopora species recruited to the reef. However, recruitment was dominated by two species: Pocillopora tuahiniensis (46%) and Pocillopora meandrina (43%). Under ambient conditions, recruitment of P. tuahiniensis and P. meandrina was similar, but experimentally reducing consumer pressure increased recruitment of P. tuahiniensis by up to 73% and reduced recruitment of P. meandrina by up to 49%. In both species, nutrient enrichment increased recruitment and colony growth rates equally, but colonies of P. tuahiniensis grew faster and were up to 25% larger after three years than those of P. meandrina, and growth was unaffected by reduced consumer pressure. Predation by excavating corallivorous fish was higher for P. meandrina than for P. tuahiniensis, especially under nutrient enrichment. In contrast, polyp extension (an indicator of elevated heterotrophic feeding as well as susceptibility and attractiveness to corallivores) was lower for P. meandrina than for P. tuahiniensis, especially under low to medium consumer pressure. Overall, we uncovered ecological differences in the response of morphologically cryptic foundation species to two pervasive stressors on coral reefs. Our results demonstrate how cryptic species respond differently to key anthropogenic stressors, which may contribute to response diversity that can support ecological resilience or increase extinction risk.