Understanding the patterns of shell reduction in turtles is relevant when examining both fossils and living forms. The soft-shelled turtles (Trionychidae) are characterized by the general reduction of the peripheral bony elements of the carapace, and some species possess structures of contested homology. By examining Remane's ‘principal criteria’, we addressed the primary homology of the prenuchal and the posterior peripheral ossicles (= PPOs) of the Asian flapshell turtles, Lissemys spp., thus evaluating their topological equivalence, their structural quality, and the presence of intermediate forms in ontogeny and phylogeny. We conducted an analysis of gross morphology, bone histology, and ontogeny of these elements in a large sample of living and fossil trionychids and their sister-group, the carettochelyids. We conclude that the prenuchal comprises a neomorphic structure that does not fulfil any of the homology criteria examined. The assessment of the homology of PPOs is less straightforward because of the presence of partly conflicting evidence. Nevertheless, PPOs and standard peripherals share an antero-posterior polarity of the ossification pattern, which we interpret as a significant shared underlying developmental pattern. Depending on the phylogenetic position of Lissemys in trionychid phylogeny, the hypothesis of PPOs homology with standard peripherals is a straightforward one or, alternatively, one involving homologous developmental processes at other levels of the hierarchy, resulting in similar microstructural characteristics of these bony shell features. In this respect, we consider the antero-posterior polarity of the ossification pattern of both PPOs and standard peripherals as providing potential evidence for the homology of the genetic control regulating the expression of both these structures, and therefore we interpret these structures as homologues on the basis of a deeply homologous underlying developmental process. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 462–476.