Organisms are made up of semiautonomous parts or modules, but identifying the limits of modules is not straightforward. Covariation between morphological features across the adults of a clade can identify suites of characters as putative modules. We contrast such an approach for delimiting modules with one that includes inferences of heterochrony, evolutionary change in the timing of developmental events. That two features show differing types of heterochrony is a strong indication that they are ontogenetically dissociated and belong to differing modules even though these features may covary across adults. We focus on xylem vessels (wood water conduits) and phloem fibers (bark support cells) in the stems of the 13 species of the plant genus Moringa (Moringaceae), which vary from massive bottle trees to tiny tuberous shrubs. Across adults, vessel diameter and number of phloem fibers scale positively and significantly with stem size and with respect to one another. This covariation across adults suggests that these features may be members of the same ontogenetic module, a finding that might be expected given that these cells both derive from the same tissue ontogenetically and are tightly functionally integrated in the stem. In contrast, ontogenetic data in the context of a phylogenetic hypothesis suggest that vessel elements and phloem fibers have undergone different types of paedomorphosis, heterochronic alteration to ontogeny producing adults of descendant species that resemble the juveniles of their ancestors. Vessels and phloem fibers would be expected to show differing types of paedomorphosis only if they are not ontogenetically coupled, and therefore it is likely that they are part of different modules; this ontogenetic independence was invisible to inference based only on adult covariation. Finally, we show reasons to implicate paedomorphosis in the diversification in life form of Moringa across the Old World dry tropics.