Phosphate and arsenate are very similar compounds, and there is great interest in studying their relationship and their interaction with biological systems. Despite having no apparent biological function, specific genes regulate arsenic interaction with cells and can be located in regions of the genome called arsenic islands, where phosphate metabolism genes are also present. Although they are neighboring genes, the nature of their relationship and how they have been selected is still unknown.In this work, we analyzed the metagenomes of the four microbial ecosystems inhabiting hypersaline lakes of the Argentine Puna and the Atacama salt flat in Chile and have evaluated the presence and abundance of both arsenic and phosphate metabolism genes. The samples analyzed included microbialites, biofilms and microbial mats; all of them established under high arsenic concentrations, high UV radiation and high temperature fluctuation, among others. The results show great differences in the dispersion and abundance of genes related to both phosphate and arsenic metabolism in the analyzed samples. The main difference is given in the Diamante Lake, located in the crater of the Galan volcano characterized by being one of the lakes with the highest arsenic concentration (2.34 mM). Correlating genes abundance with the physicochemical parameters of the lakes studied, our results suggest that arsenic and phosphate metabolism are intricately co-regulated in environmental conditions.