Thin fossil eggshell from Upper Cretaceous deposits of Europe, characterized by nodular ornamentation similar to modern gekkotan eggshell, has mostly been interpreted as gekkotan (=‘geckoid’) in origin. However, in some cases, as for the oogenus Pseudogeckoolithus, a theropod affinity has also been suggested. The true affinity of these fossil ‘geckoid’ eggshells has remained controversial due to the absence of analytical methods for identifying genuine gecko eggshell in the fossil record. In this study, we apply electron backscatter diffraction (EBSD) analysis to latest Cretaceous European ‘geckoid’ (including Pseudogeckoolithus) eggshell, in comparison with modern gekkotan and theropod (avian) eggshell. We found that Pseudogeckoolithus has a definite theropod eggshell‐like crystallographic configuration, in clear contrast to that seen in modern ‘gecko eggshells’. Furthermore, the crystallography of the nodular ornamentation in Pseudogeckoolithus is similar to that seen in megapode eggshell, but different from that of gecko eggshell, 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, the present results suggest caution about the dangers of using potentially homoplastic eggshell characters in eggshell parataxonomy.