Invasive alien species severely impact native and endemic species, disproportionately affecting insular species, and this is especially true for Caribbean reptiles. The Lesser Antillean iguana (Iguana delicatissima) experienced a drastic range decline strongly driven by hybridization with non-native green iguanas (NNGI,Iguana iguanaspecies complex). With numerous NNGI populations within the Lesser Antilles, it is a matter of time before these arrive on the lastI. delicatisismainhabited islands, whereupon rapid in-situ identification of non-native and hybrid animals is essential. However, only a few scale and coloration characters allow in-situ identification of NNGI, which are compromised by introgression. Here we assessed the differentiating power of an additional 20 scale and length-dependent characteristics between theI. delicatissimapopulation on St. Eustatius and the established NNGI population on St. Maarten, the main source of arriving stowaway iguanas on St. Eustatius. We identified 14 length-dependent characteristics that significantly differ betweenI. delicatissimaand NNGI’s, with multi-variate analysis showing clear morphospace separation and high assignment accuracy of predictive models (>91%). Additionally, the number of femorals and supra digital scales significantly differs between these iguanas. Morphospace knowledge of St. Eustatius’I. delicatissimanow allows rapid identification of any divergent iguanas using easy to obtain measurements and meristics. Given intraspecific variation inI. delicatissimaand green iguanas, we recommend that these characteristics are assessed and validated for other populations, including hybrid individuals. Our work demonstrates the urgent need to invest in baseline morphometric datasets to aid rapid in-situ conservation efforts once NNGI arrive and start to hybridize withI. delicatissima.