Aigialosaurs have been recognised as a group of semi-aquatic marine reptiles for over one hundred years. While the taxonomic status of aigialosaurs has changed little in the past century, the interfamilial relationships have been modified considerably making the phylogenetic relationships between aigialosaurs, mosasaurs, dolichosaurs, coniasaurs, varanids and other squamates a topic of much debate. The monophyly of the family Aigialosauridae has been contested by recent studies and remains highly questionable. The higher-level relationships of mosasauroids within Squamata remain problematic with studies placing mosasauroids outside of Varanidae, Varanoidea and even Anguimorpha. These findings conflict with earlier views that aigialosaurs (and by association mosasaurs) were closely related to Varanus. This study concludes that further descriptions of aigialosaur taxa are needed, and several key flaws need to be addressed in the data matrices that have been used in previous studies. This should facilitate the clarification of aigialosaur systematic relationships both within Mosasauroidea and Squamata.