Prolonged drought and salinity on the Chowilla floodplain of the Murray River have caused deterioration of E. largiflorens F.Muell. A putative hybrid with E. gracilis F.Muell, green box, withstands the saline conditions. We aimed to substantiate that green box is a hybrid and to test for agreement between morphological and physiological characters with amplified fragment length polymorphisms (AFLP). Mature stands were measured for leaf, trunk, floral, cotyledon, carbon and nitrogen isotope discrimination, specific leaf area (SLA) and AFLP. Green box was placed between E. largiflorens and E. gracilis according to categorical principal components analysis (CATPCA) of 21 morphological and physiological characters and character states. The hybrid index of 11 AFLP markers that were 78% species specific separated E. gracilis and E. largiflorens, and the majority of green box plants displayed indices ranging from 0.42 to 0.53, reflecting mostly additive inheritance. Calculation of the hybrid index with all 232 AFLP markers, using maximum likelihood, similarly placed green box between E. gracilis and E. largiflorens. Our morphological, physiological and AFLP-marker observations substantiated that green box is a hybrid between E. largiflorens and E. gracilis.