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• Spanish pepper landraces still lack exhaustive characterization. • Conventional and digital traits are useful for pepper germplasm characterization. • Digital traits have a higher differentiating ability than conventional descriptors. • Fruits are responsible for most of variability within C. annuum varieties. • Typification of these materials is highly relevant for peppers breeding programs. Spain is a relevant secondary centre of diversity for Capsicum annuum peppers, especially for the bell types known as Pimiento Morrón or Pimiento de Morro. Thus, a myriad of highly regarded landraces adapted to a wide range of conditions can be found throughout the country, as a result of centuries of farmers breeding. Despite that, these materials lack of proper characterization, of paramount importance for farmers, breeders and germplasm management. In this regard, in addition to internationally accepted conventional descriptors, high-throughput digital phenotyping tools like Tomato Analyzer, a software originally developed to process scanned images of cut tomato fruits and to record a range of morphological parameters, may provide an important help towards exhaustive germplasm characterization. With this aim, 32 conventional and 35 Tomato Analyzer digital traits were used herein to characterize a large collection of C. annuum accessions from all Spanish regions, including Protected Designations of Origin and Protected Geographical Indications, with emphasis on Morrón peppers, in order to assess the diversity within Spanish elite germplasm and to test the efficiency of those methods to differentiate varietal types and closely related materials. A considerable amount of variation was found using both conventional and digital traits, even within Morrón pepper groups, reflecting the diversity of Spanish peppers in terms of plant and fruit morphology, essential for future breeding programs. Both conventional descriptors and digital parameters were able to distinguish varietal groups. However, on the whole, digital phenotyping was able to discriminate in a more accurate way. Most digital parameters were able to discriminate varietal groups into higher numbers of categories (≥4) than conventional traits (usually 2–4). In addition, the number of significant pairwise differences among varietal groups was considerably higher for digital parameters than for conventional descriptors, enabling a powerful separation, particularly relevant for closely related groups such as Morrón peppers. Likewise, as revealed by Principal Components Analysis, digital phenotyping allowed a more powerful intra-varietal separation compared to conventional descriptors. Finally, a subset of 4 conventional descriptors and 13 Tomato Analyzer traits were identified as the most discriminant to distinguish among closely related C. annuum accessions, explaining 81.81 % of total variance found by Principal Components Analysis. Fruit traits explained the highest percentage of variance for our collection. [ABSTRACT FROM AUTHOR]