A naturally occurring putative hybrid between Eucalyptus largiflorens F. Muell and Eucalyptus gracilis F. Muell called Green Box tolerates saline conditions of the River Murray floodplains better than E. largiflorens. Revegetation strategies utilizing seedlings of Green Box have had limited success because only a few are Green Box and the majority are throw backs to E. gracilis and E. largiflorens. Therefore, the purpose of this study was to identify traits characteristic of Green Box and AFLP markers associated with the traits enabling selection at the seedling stage. This was done by non-linear canonical correlation analysis (OVERALS) to test for statistically significant associations between morphological and physiological traits with 232 AFLP markers from 9 primer combinations. OVERALS with all markers produced 1st and 2nd dimensions accounting for 80 and 74% of variation respectively. Green Box plants were placed intermediate between E. gracillis and E. largiflorens according to leaf colour, gloss and nitrogen with component loadings (lc) of 0.340, 0.615 and 0.294 respectively. A second approach of simple linear regression of morphological and physiological traits against all 232 AFLP markers singled out 17 with significance P<0.05. Thirteen of these were also identified by OVERALS. Four occurred with high frequency in Green Box and E. largiflorens distinguishing them from E. gracilis. In order to separate Green Box and E. largiflorens, the segregation of a further three markers can be used to align Green Box with E. gracilis. Therefore, the segregation of 7 markers can be utilized to select Green Box.