ABSTRACT: The repetitive clonal growth of the seagrasses Zostera noltii Hornem. and Cymodocea nodosa Aschers at the module level was used to implement a deterministic, individual-based, numerical model using the simplest growth rules. Inter- and intraspecific variability in plant morphology and meadow attributes was simulated, and the results yielded by the model were compared with an existing large data set recorded for both species. The model outputs showed that intra- and interspecific morphological variability can be accurately described (r = 0.99, p < 0.0001, n = 19) by a restricted number of parameters (plastochrone interval [PI] and elongation rates for rhizome [RER] and leaf [LER], which are species-specific parameters). Interspecific differences in meadow properties were recorded; however, simulated values were double those observed. This result was mainly attributable to a lack of density-dependence phenomena in the model assumptions, revealing the importance of such phenomena in structuring seagrass populations. In general, species with high PIs displayed longer modules (leaves and internodes) and lower shoot densities, whereas species with lower PI values developed shorter modules and crowded stands. This result corresponds with the relationship indicated by the self-thinning law and by previous studies. The model also showed that plant morphology arises as an emergent property of a simple set of growth rules acting at the module level, and that plant dynamic parameters can be tuned by seagrasses in response to their local environmental conditions. Thus, the whole-plant response to the environment can be determined by the sum of all the modular responses. This model, together with a better knowledge of the regulation of plant dynamic parameters by control variables (light, temperature, nutrients, etc.), provides a conceptual framework that allows the incorporation of module, plant morphology and meadow properties into functional–structural seagrass models, in which feedbacks among plant morphology, plant development and phylloclimate (i.e. the physical environment actually perceived by each individual organ or plant population) can be included.