Actinopterygians demonstrate high levels of morphological disparity, especially in the variation of fin positions, sizes and shapes. One hypothesis to explain the diversity of fin morphologies is that it is facilitated by a modular organization. According to this hypothesis, fin modules would be quasi-independent during ontogeny or evolution, facilitating their evolvability. We investigated variational modularity of fins in two cyprinid species, the zebrafish (Danio rerio) and the Northern redbelly dace (Chrosomus eos), to determine which subsets of fins are quasi-independent and which are most highly integrated in positioning. Hypotheses of modularity were evaluated using a combination of methods suitable for analyses of landmarks. The hypothesis that the dorsal and anal fins belong to a posterior trunk and tail module is strongly supported, a finding that can be explained by the use of subcarangiform locomotion in these two species. There is also some support for the hypothesis that the paired fins and head region each constitute variational modules. The support for fin variational modules is weaker than expected considering the wealth of developmental evidence supporting fin modularity. This might be related to a dissociation of the fin positioning modules during actinopterygian evolution, a process that had already been suggested for the dorsal and anal fins. Alternatively, the fin modules inferred from developmental data might not directly translate into variational modules: variational modules can incorporate the signals from numerous partially overlapping developmental processes so that one to one correspondence between developmental and variational modules is not always expected.