One hundred and twenty Spanish landraces of peas (Pisum sativum L.) collected in different micro-climatic areas, together with three commercial varieties and one breeding line, were subjected to molecular characterization using Inter Simple Sequence Repeat (ISSR) amplification. Landraces originated from 7 to 1427 m asl. Most accessions were collected in temperate areas with dry Mediterranean humidity regimes. ISSR markers detected high levels of variability between accessions and were useful for identification of individuals and clarification of genetic relationships between them. The 18 groups obtained with molecular data were not significantly related to 21 agro/climatic regions. Clustering based on climatic and ISSR characters differed because the data types present different aspects of genetic diversity. These results will be applied to establish a pea core collection at the Plant Genetic Resources Centre of the Spanish National Institute of Agriculture and Food Research and Technology (CRF-INIA).