Background: The establishment of the metagenomics seems a suitable approach to assess the abundance and diversity of antibiotic resistance genes (ARG) Methods: Metagenomics study in a Peruvian city from the highlands, where samples derived from sewage waters from two hospitals and the urban setting. DNA extraction was performed in 250 mL and then16S rRNA gene amplification and shotgun sequencing were carried out. The bioinformatic pipeline was performed following recommendations for metagenomics analysis. Alpha diversity was evaluated with the Shannon and Simpsons indices; whereas beta diversity was evaluated through the Bray-Curtis index, and using the principal coordinate analysis (PCoA) to explore and visualize the differences. Results: We found a high abundance of bacteria related to resistance to beta-lactams, macrolides, aminoglycosides, fluoroquinolones and tetracyclines. The urban sample did not differ significantly from the wastewater ARG presence from the hospitals in Huanuco. Conclusion: Metagenomics analysis through sewage strategies seems to help to monitor the AMR to establish local public health policies, especially in cities or countries with limited resources to establish large projects conceiving the One Health approach.