We characterized a population of hybrids between English walnut and Northern California black walnut (Juglans regia X J. hindsii) and their backcrosses (BC) using both genomic markers and morphological traits. ANOVA and regression methods were used on three years' data to identify a subset of five variables that describe the morphological variability among backcross populations and their parents (R2 = 0.89). Genomic markers were identified using randomly amplified polymorphic DNA (RAPD). A subset of 60 markers specific to the donor species (J. hindsii) were scored in 50 backcrosses to estimate the percent recipient genome in each evaluated BC. The backcrosses were ranked using each method of evaluation; correlation between the ranks was 0.423 and highly significant. Each evaluation method has advantages but neither was able to reliably identify elite progeny.