The Coffea genus includes about 124 species, of which Coffea arabica L. and Coffea canephora Pierre ex A. Froehner are the most commercially important, supplying 63 and 37% of the world coffee production, respectively. C. arabica L. is associated with better cup quality, but presents serious problems with pests and diseases, potentiated by climate change. The development of new varieties of C. arabica L. requires the inclusion of genetic diversity, looking for incorporating new genes to tolerate or resist the most important pests and diseases, maintaining or improving yield and cup quality of the new materials. The technology of diversity arrays based on sequencing (DArTseq™) allows the rapid identification of the single nucleotide polymorphism (SNP) for a genomic approach of genetic diversity. The objectives of the present study were: (1) to evaluate the diversity and genetic structure of a central coffee collection of the Mexican National Bank of Coffee Germplasm; (2) assess the reproducibility and error rates of the markers and their broad representation in the genome and (3) to propose a new collection with representative and divergent promising genotypes for stablishing a coffee breeding program in Mexico. 87 coffee accessions of three different species of the Coffea genus were sequenced and 16,995 SNP markers were derived from 34,000 unique sequences obtained by the DArTseq™ method. After removing the markers with more than 10% of missing data and the MAF < 5%, we end up with 1739 polymorphic SNP markers for the analysis. A dendrogram was generated which divided the accessions into five divergent groups where promising genotypes were identified. In conclusion, there is genetic diversity among the accessions of Coffea spp. for use in future breeding programs.