Neltuma pallida (Fabaceae), also known as “algarrobo” is an important tree in the dry forest of Peru since it is a source of livestock fodder, human food and fuelwood, among others. To date, the genetic composition and population structure of this legume in Peru remains unknown. Currently, it is possible to explore genetic parameters of plants with reliable and modern methods like genotyping-by-sequencing (GBS). We here for the first time used single nucleotide polymorphisms (SNPs) markers to infer the genetic diversity and population structure of 87 accessions of algarrobo from two northern Peruvian regions that comprise part of the dry forest ecosystem, Piura and Tumbes. A total of 967 SNPs distributed along all chromosomes of algarrobo were identified. Similar to previous studies, a discriminant analysis of principal components showed weak population genetic structure among these individuals. A dendrogram was generated using the UPGMA clustering algorithm and, similar to the principal coordinate analysis (PCoA), it showed no geographic component. Nei's gene diversity was 0.4, and a negative Fis for algarrobo population was detected, demonstrating that it also depends on cross-pollination. We hope that this information is the beginning of the path towards the development of conservation strategies and modern breeding of this important legume.