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Ultraviolet radiation (UVR) may cause significant DNA damages when interacting with shallow water organisms, primarily in the tropics. Here we investigate DNA repair kinetics in two shallow water colonial marine invertebrates, the scleractinian coral Seriatopora hystrix and the colonial tunicate Botryllus schlosseri. Cells from both species were irradiated with UVA/UVB in vitro. Using the alkaline (B. schlosseri) and the neutral (S. hystrix) versions of the comet assay, DNA damage and repair were measured. After 24 h, little DNA repair was recorded in the irradiated Botryllus cells for both types of radiation (UVB 3.55 W/s/UVA 8.09 W/s, 15 min radiation each), revealing twice (30%) as much apoptotic cells as controls. Cells of S. hystrix showed a highly efficient DNA repair capacity (i.e. complete DNA repair within 30 min post-irradiation), coincident with their endurance to reactive oxygen species impacts. Therefore, while S. hystrix and likely other shallow water corals use efficient DNA repair mechanisms, B. schlosseri and possibly other similar species are reliant on UVR sheltered sites to maintain DNA integrity. The low repair capacity of B. schlosseri might be explained by the ‘disposable soma’ concept, where zooidal soma in this species is cast off and recycled on a weekly basis. Further research is needed to elucidate the spectrum of responses used by shallow water sedentary marine invertebrates to cope with daily high UVR levels.