Field evaluations were conducted of pecan [Carya illinoinensis (Wangenh.) C. Koch] trees regenerated via somatic embryogenesis to assess if the trees maintained clonal fidelity and exhibited true-to-type characteristics. Phenotypic and molecular comparisons were made of trees from two different tissue culture lines after 4 years in the field. Factors evaluated included shoot growth, leaf morphology, and susceptibility to fungal scab [Cladosporium caryigenum (Ellis & Langl.) Gottwald] and southern pecan leaf phylloxera (Phylloxera russellae Stoetzel). Genetic fidelity was examined using amplified fragment length polymorphism (AFLP) analysis. Statistically significant differences were observed between the culture lines in phenotypic leaf characteristics (i.e., specific leaf weight and leaf length-to-width ratio), number of shoots per 1-year-old branch, and in the frequency of scab lesions on leaves. No between-line differences were observed in trunk caliper, average and total shoot growth, shoot length per cross-sectional area, or presence of phylloxera galls. AFLP analysis readily detected differences between culture lines. Cluster analysis generally grouped trees together that were regenerated from the same line. Trees within a culture line usually exhibited similar leaf characteristics, but not shoot growth or tree height. A few trees exhibited more extreme leaf characteristics and differed from each other. However, they were statistically similar to most of the other trees in the population evaluated. AFLP data revealed that some trees exhibited greater divergence and less similarity than other trees from the same line. The nature and significance of such variation at this time are not related to any detectable phenotypic differences.