Thin fossil eggshells from Upper Cretaceous deposits of Europe, characterized by nodular ornamentation similar to modern gekkotan eggshells, have mostly been interpreted as gekkotan (=‘geckoid’) in origin. However, in some cases, like the oogenus Pseudogeckoolithus, their theropod affinity was also suggested. The true affinity of these fossil ‘geckoid’ eggshells remained controversial due to the absence of analytical methods effective in identifying genuine gecko eggshells in the fossil record. In this study, we apply electron backscatter diffraction (EBSD) analysis to latest Cretaceous European 'geckoid' (including Pseudogeckoolithus) eggshells, in comparison with modern gekkotan and theropod (avian) eggshells. Our results show that Pseudogeckoolithus has a definite theropod eggshell-like crystallographic configuration, in clear contrast to that seen in modern geckos. Furthermore, the crystallography of the nodular ornamentation in Pseudogeckoolithus is comparable to that seen in megapode eggshells, but different from that of gecko eggshells, despite superficial morphological similarity. The remarkable morphological similarities between Pseudogeckoolithus and modern gecko eggshells are thus convergent, and the ‘gekkotan affinity’ hypothesis can be dismissed for Pseudogeckoolithus. This study provides a template for differentiating true gekkotan from dinosaurian eggshells in the fossil record. The potential functional significance of eggshell ornamentation, lost in most modern birds, requires further study, and experimental zoological approach may shed light on this issue. Finally, our results caution about the dangers of using potentially homoplastic eggshell characters in eggshell parataxonomy.