Availability of standardized morphological and molecular characterization data is essential for the efficient development of breeding programmes in emerging crops. Pepino (Solanum muricatum) is an increasingly important vegetatively propagated vegetable crop for which concurrent data on morphological descriptors and molecular markers are not available. We evaluated 58 morphological traits, using a collection of 14 accessions of pepinos (including local Andean varieties and modern cultivars) and 8 of wild relatives, using the IPGRI and COMAV descriptors lists coupled with 20 EST-SSRs from tomato. High morphological diversity was found in both cultivated and wild accessions; all morphological traits except three were variable. Cultivated pepino and wild relatives were significantly different for 26 traits. Also, local varieties and modern cultivars of pepino were different from each other for 13 morphological traits and were clearly separated in a principal components analysis. Fourteen of the 20 tomato EST-SSRs were polymorphic, with an average number of alleles per locus of 4.07 and a polymorphic information content value of 0.4132. This revealed a high degree of transferability from tomato to pepino and wide molecular diversity in the collection. Cultivated materials manifest high levels of observed heterozygosity, suggesting that it is related to heterosis for yield associated with heterozygosis. SSR data clearly differentiated cultivated and wild materials. Furthermore, for pepinos, the modern varieties were genetically much less diverse than the traditional local varieties. However, both groups of cultivated material expressed a low degree of genetic differentiation. A strong correlation (r = 0.673) between morphological and molecular distances was found. Our results provide foundational information for programmes of germplasm conservation, and that can be used to enhance breeding for this emerging crop. ; Herraiz García, FJ.; Vilanova Navarro, S.; Andújar, I.; Torrent Martí, D.; Plazas Ávila, MDLO.; Gramazio, P.; Prohens Tomás, J. (2015). Morphological and molecular characterization of local varieties, modern cultivars and wild relatives of an emerging vegetable crop, the pepino (Solanum muricatum), provides insight into its diversity, relationships and breeding history. Euphytica. 206(2):301-318. doi:10.1007/s10681-015-1454-8. ; Senia ; 301 ; 318 ; 206 ; 2