Penjar tomato is a varietal type cultivated in northeast Spain that characteristically has a long shelf life, small fruit, and wide morphological variability among cultivars. To determine the genetic basis for the long shelf life in the Penjar varietal type and to describe the genetic background and agromorphologic characteristics of the group, we studied 27 Penjar accessions representative of the entire range of variation in traits related to agronomic behavior, fruit morphology, and sensory quality. We found that the long shelf life of Penjar (mean: 126.8 days) is due to the ripening mutant alcobaça (alc), and the molecular basis of this mutation is the replacement of thymine by adenine in position 317 of the coding sequence of the NAC.NOR gene; thus, alcobaça (alc) is an allele of non-ripening (nor). The amplified fragment length polymorphism (AFLP) study found 18.07% polymorphic loci within the Penjar varietal type, which is higher than usual in landraces. The variation in agronomic and morphologic traits between accessions was also very high; thus, the heterogeneity of the Penjar group probably results from the introduction of the allele alc in distinct landraces. Our results also show that in germplasm containing the alc mutation shelf life is negatively correlated with fruit size (weight, width, length, and number of locules); thus, the predominance of small fruit within the varietal type is probably the result of this trait being dragged along in the selection for long shelf life.