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Biofouling causes massive economical losses in the maritime sector creating an urgent need for effective and ecologically non-harmful antifouling materials. Zinc oxide (ZnO) nanorod coatings show promise as an antifouling material; however, the toxicity of ZnO nanorods to marine organisms is not known. We compared the toxicity of suspended ZnO nanorods (NR) with that of ZnO nanoparticles (NP) and ionic Zn2+ in a marine bivalve Mytilus edulis exposed for two weeks to 10 or 100 µg Zn L-1 of ZnO NPs, NRs or Zn2+, or to immobilized NRs. The multi-biomarker assessment included bioenergetics markers (tissue energy reserves, activity of mitochondrial electron transport system and autophagic enzymes), expression of apoptotic and inflammatory genes, and general stress biomarkers (oxidative lesions, lysosomal membrane stability and metallothionein expression). Exposure to ZnO NPs, NRs and Zn2+ caused accumulation of oxidative lesions in proteins and lipids, stimulated autophagy, and led to lysosomal membrane destabilization indicating toxicity. However, these responses were not specific for the form of Zn (NPs, NR or Zn2+) and showed no monotonous increase with increasing Zn concentrations in the experimental exposures. No strong disturbance of the energy status was found in the mussels exposed to ZnO NPs, NRs, or Zn2+. Exposure to ZnO NPs and NRs led to a strong induction of apoptosis- and inflammation-related genes, which was not seen in Zn2+ exposures. Based on the integrated biomarker response, the overall toxicity as well as the pro-apoptotic and pro-inflammatory action was stronger in ZnO NPs compared with the NRs. Given the stability of ZnO NR coatings and the relatively low toxicity of suspended ZnO NR, ZnO NR coating might be considered a promising low-toxicity material for antifouling paints.