Drug resistance remains a major concern in leishmaniasis chemotherapy, a neglected tropical disease that causes 60,000 deaths around the world annually. To better understand the molecular mechanisms behind drug resistance, we selected L. guyanensis parasites resistant to antimony, the first-line drug against this disease in many countries. Through whole-genome sequencing we found variations in the copy number of chromosomes in addition to gene amplification and gene deletion events in antimony-resistant parasites. A marker previously related to antimony resistance, the gene coding for multidrug resistant protein A, was found to be amplified. Transport studies revealed a reduced antimony accumulation in resistant parasites that we correlated with the deletion of the gene coding for the aquaglyceroporin 1 (AQP1) responsible for antimony uptake in Leishmania. Additionally, a point mutation in AQP1 was found to be associated with antimony resistance. These findings may contribute to the development of new chemotherapy strategies against leishmaniasis.