Little experimental evidence of multiple generations of inbreeding depression is available for marine invertebrates. Here, we report that two generations of inbreeding significantly reduced larval growth and metamorphosis, but did not significantly impact fertilization and hatching in the sea urchin Strongylocentrotus intermedius. A higher inbreeding coefficient had significantly more negative impacts on some traits of S. intermedius larvae (for example, larval length) but not all. Maternal effects of inbreeding depression probably appear in the eight-arm stage and metamorphosis of S. intermedius. The present study provides convincing evidence of inbreeding depression on larval growth and metamorphosis in S. intermedius and highlights the importance of avoiding multiple generations of inbreeding in sea urchin aquaculture. Statement of relevanceMultiple inbreeding dramatically impacts aquaculture of marine species. Here, we investigated effects of second generation of inbreeding on fertilization, hatching, larval growth and metamorphosis in sea urchins. The present study provides the convincing evidence on the inbreeding depression of larval growth and metamorphosis in sea urchins and highlights the importance of avoiding multiple generation of inbreeding in sea urchin aquaculture.