In agriculture and horticulture, the genetic purity of cultivars is critical to farmers, plant breeders, and seed producers as well as regulatory agencies. Cultivar identification by seed protein polymorphism and computer analysis of images of plant characters is an alternative method for cultivar identification. Comparison of the efficiency and precision of identification of varieties of tomato by gel electrophoresis of seed protein and digital processing of scanning electron microscope (SEM) images of stomata were made. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) technique for seed protein profile was useful in distinguishing tomato (Solanum lycopersicum L.) varieties. Digital processing of SEM images of stomata created four clusters depending on the percentage circularity, or how well the image fits a circle, of the stomata. Both methods could identify varieties with high contrast in stomatal characters and protein banding pattern, although digital processing of SEM images of stomata was less precise in distinguishing varieties with less contrast. Protein markers and digital processing of important plant morphological images may be utilized to distinguish varieties of tomato. © Taylor & Francis Group, LLC.