SummaryCongenital malformations of the eye comprise a wide spectrum of developmental defects. Anophthalmia‐microphthalmia (AM) is the most severe end of these conditions. The different ocular malformations are thought to be part of an overlapping spectrum of embryonic developmental defects. Phenotypic overlap is emphasized by molecular results demonstrating that the same genes may lead to variable defects. We aimed at delineating the molecular bases of AM in order to improve knowledge on eye development as well as patient care. We follow one of the largest cohort of ocular developmental defects cases with extensive clinical and genetic analyses and report here extensive genetics analysis delineating a valuable genetic epidemiology of AM triggering genes. To date a genetic cause is identified in less than half of the patients suffering AM. The most likely explanation for this is that only a small proportion of causative genes have been identified. That is, we report here the strategy used to identify novel AM genes among rare and mainly sporadic patients. This led highlighting the malformation spectrum of already known genes and delineating original pathways respectively involved in retinoic acid metabolism and Sonic Hedgehog signalling.