Two commonly reported Frustulia morphospecies from oligotrophic habitats, F. crassinervia and F. saxonica, showed overlapping morphological variation within natural populations and between clonal strains representing different genetic entities. Therefore, morphologies of natural populations of the F. crassinervia-saxonica complex were analyzed using geometric morphometric techniques regardless of species or genetic identity. It has been examined whether shape, centroid size, morphological diversity, and globularity of valves from three types of peatland habitats representing ombro-minerotrophic gradient reflected ecological differentiation within the Frustulia crassinervia-saxonica species complex. Morphometric analyses showed that valve differences within the species complex were significantly correlated with environmental conditions. In particular, allometric shape changes and size of valves showed strong relationships with different types of peatland habitats. It has been suggested that allometry probably acts as a constraint on morphological plasticity and is canalizing microevolutionary morphological differentiation within the F. crassinervia-saxonica complex.