Spain is one of the most important centers of diversity for Capsicum annuum peppers, and a plethora of ecotypes can be found throughout the country. These resources represent a valuable genetic pool which must be characterized in depth both morphologically and molecularly. The aim of the present work was to assess phenotypic and genotypic diversity and relationships within some Spanish pepper landraces. A collection of 12 Spanish pepper landraces and 15 foreign controls was characterized with a set of 46 descriptors from International Plant Genetic Resources Institute (IPGRI, now Bioversity International) and genotyped using Genotyping-by-Sequencing (GBS). The studied collection was genetically diverse. The morphological characterization allowed discrimination of the varieties through fruit size, growth habit and others traits. SNP-based phylogenetics clustered together Spanish accessions. Our results provide useful information of several different ecotypes to boost breeding programs.