The aerial epidermis of plants plays a major role in their environment interactions, and the development of its cellular components -trichomes, stomata and pavement cells- is still not fully understood. We have performed a detailed screen of the leaf epidermis of two generations of the well-established Solanum pennellii ac. LA716 x Solanum lycopersicum cv. M82 introgression line (IL) population using a combination of scanning electron microscopy techniques. Quantification of the trichome and stomatal densities in the ILs revealed 18 genomic regions with a low trichome density and 4 ILs with a high stomatal density. We also found ILs with abnormal proportions of different trichome types and aberrant trichome morphologies. This work has led to the identification of new, unexplored genomic regions with roles in trichome and stomatal formation and provides an important dataset for further studies on tomato epidermal development that is publically available to the research community.