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Abstract Hybridization is among the main threats posed by invasive alien species (IAS) and can lead to extinction of endangered species. Here we focus on insular native populations of Iguana in the Lesser Antilles that are threatened by hybridization with non-native green iguanas (NNGI) through genetic swamping and eventual extinction. Whilst much effort is put towards preventing NNGI incursions and these subsequent processes, their underlying mechanims are poorly understood. We collected data on snout-vent length (SVL), tail length (TL) and clutch size during an eradication program of hybrid and non-native iguanas on the island of Saba. First, we genetically assessed the status (native/hybrid/non-native) of all individuals from Saba. Subsequently, we combined these data with total length (SVL+TL) data from NNGI on St. Martin (source of NNGI on Saba), and SVL and clutch size from native insular and mainland Iguana populations. We found that hybrids on Saba produce significantly larger clutches than native Saba iguanas with a similar SVL, and even larger than one mainland population. However, comparisons of total length between native and hybrid Saba iguanas and NNGI from St. Martin indicate that native iguanas are only significantly smaller than NNGI, not compared to hybrids. Our results suggest that declines in native Iguana populations are at least partially driven by genetic swamping, through larger clutch sizes of NNGI as well as larger clutch sizes of hybrid iguanas compared to native iguanas. To optimize long-term conservation maintaining intraspecific genetic diversity is critical and we thus urge rapid identification and protection of remaining native iguanas within populations heavily impacted by hybridization with NNGI (e.g., Grenada, Guadeloupe, and Martinique).