The Peruvian Paso Horse (PPH) is a breed native to Peru. It is important socially and economically and is classified as a flagship product. However, very little is known about its genetics, thus limiting the development of a genetic improvement program and conservation. Even though genomic tools are widely available for different animal species of importance, such as horses and cattle, the PPH remains abandoned. Moreover, its phylogenetic relationship, together with the genetic and population structure components of the PPH, are still limited. Here, we sequenced the whole genome of a representative individual of the PPH using long and short reads and obtained 160 GB and 74 Gb of raw data, respectively. Hi-C sequencing will show the three-dimensional chromosome structure of this breed, and RNA-Seq reads will determine its gene expression. In addition, a total of 150 hair samples from the tail and mane of the PPH were recently collected in the geographic departments of Lima and Arequipa in order to genotype them with an SNP chip, attempting to determine the genetic structure and diversity of this Peruvian breed. Currently, we are in the process of sending the DNA samples to an external service. In the meantime, we are using different bioinformatic tools to assemble and annotate the mitochondrial and whole genome of the PPH. We expect to obtain our final results before the year comes to an end. Finally, the use of these modern tools may stimulate other Peruvian researchers to study our abundant zoogenetic resources for conservation and breeding purposes, promoting their sustainable use.