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Among nest-holding fish, males often choose nest sites according to their own body size (i.e. size-assortative nest choice). In most cases, this can be explained by intrasexual competition. However, a few studies, for example on a marine population of the sand goby, Pomatoschistus minutus, have found a size-assortative nest preference, even when intrasexual competition is excluded. We conducted three aquarium experiments, using small sand goby males (47–54 mm) that were given either small (size-matched) or large (size-mismatched) nest sites, to test for potential mechanisms underlying this size-assortative nest choice in the absence of intrasexual competition. The three mechanisms investigated were (1) female preference, (2) paternal expenditure and (3) nest take-over. We did not, however, find any fitness advantages for size-matched males in any of the three experiments, suggesting that some other mechanism, such as defence against egg predators, is underlying this particular behaviour. Thus, further studies are needed to explain size-assortative nest choice behaviour in the sand goby.