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Invasive alien species are among the main drivers of the ongoing sixth mass extinction wave, especially affecting island populations. Although the Caribbean is well‐known for its high species richness and endemism, also for reptiles, equally important is the regional contribution of non‐native species to island biodiversity. The Lesser Antilles encompass high genetic diversity in Iguana, though most native populations either have gone extinct or are declining following competitive hybridization with invasive non‐native green iguanas. Here, we assessed non‐native presence in two poorly‐studied native melanistic Iguana iguana populations using available genetic tools and explored utilizing size‐dependent body measurements to discriminate between native and non‐native iguanas. Genetic samples from Saba and Montserrat were genotyped across 17 microsatellite loci with STRUCTURE, and multivariate analyses indicating non‐native iguana presence only on Saba. This was corroborated by mtDNA and nDNA sequences, highlighting a non‐native origin in Central America and the ABC islands. We identified preliminary evidence suggestive of hybridization. Morphological variation among size‐dependent characteristics showed that non‐native iguanas have significantly larger subtympanic plates than native iguanas. Non‐native individuals also differed in scalation and coloration patterns. Overall, our findings demonstrate the need for continuous monitoring of non‐native iguanas within remaining native Iguana populations in the Lesser Antilles, as those not directly threatened by non‐native green iguanas are restricted to only 8.7% of the historic range. Although genetic data allow for the identification of non‐native or hybrid iguana presence, this field‐to‐lab workflow is time‐consuming. Rapid in‐situ identification of non‐native individuals is crucial for conservation management. In addition to patterns of scalation and coloration, we have highlighted the utility of size‐dependent variables for rapid diagnosis. We urge regional partners to build morphometric databases for native Iguana populations allowing the quick detection of future incursions of non‐native green iguanas and the rapid implementation of effective countermeasures during the early phase of invasion. [ABSTRACT FROM AUTHOR]