Actinopterygians are the most diversified clade of extant vertebrates. They have successfully colonized most aquatic environments, and their impressive morphological disparity bears witness to this ecological diversity. An intrinsic property of biological organization thought to facilitate morphological diversification is modularity. Indeed, the quasi-independence of some anatomical/morphological units has been suggested to increase the evolvability of organisms and the morphological disparity. The main goal of the present study is to quantify patterns of variational modularity in a model actinopterygian, the zebrafish (Danio rerio), using 3D geometric morphometrics on osteological structures isolated from micro-CT-scan data. 72 landmarks were digitalized along the cranial and postcranial ossified regions of 30 specimens of adult zebrafish. Modularity hypotheses were tested using two methods, the covariance ratio and graphical modelling. The hypothesis of the paired fins constituting a variational module is strongly supported, as well as the hypothesis of median and caudal fins forming another module, which may be associated to the subcarangiform locomotion of zebrafishes. The skull showed relatively weak overall integration, but it was tightly integrated with the rest of the body. This may suggest that the cranium is a modular structure, yet that some elements remain functionally integrated with postcranial regions. Our results provide additional support for the recognition of similar modular hypotheses that had already been identified based on the external morphology of various teleosts. Thus, the internal and external modularity patterns are congruent and at least two variational modules have been identified.