The sea louse (Caligus rogercresseyi) is a marine ectoparasite that has become one of the main constrains for the sustainable development of Chilean salmon aquaculture. Besides the well-known deleterious effects of sea lice in salmon farming, novel evidence suggests the presence of a large and diverse microbiota in the parasite. However, the biological roles in the parasite development and the potential threats for salmon farming remains unexplored. In this scenario the present work was aimed to (i) characterize sea lice microbiota from distant populations, (ii) to predict biological roles of the microbial community in the development of sea lice, and to, (iii) to identify bacterial pathogens that could potentially impact salmon aquaculture. To do this, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the C. rogercresseyi microbiota, while nanopore sequencing of the full 16S rRNA gene was used for microbial profiling at specie level. Through Hi-C we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen Tenacibacullum ovolyticum (97.87% completeness), followed by Dokdonia sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the T. ovolyticum genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between C. rogercresseyi and its associated microbiota. Regarding possible bacterial pathogens in sea lice microbiota, a total of 30 potential fish bacterial pathogens species were identified. Notably, fourteen Vibrio spp. were predominantly found in the Los Lagos region, while six Tenacibaculum spp. were more equally distributed among the sites. A core of five fish pathogens was observed in all farming zones, including Aliivibrio wodanis, T. dicentrarchi, T. ovolyticum, T. soleae, and V. splendidus (see figure). Overall, our results evidence that sea lice microbiota might fulfill key metabolic roles in the parasite’s development. At the same time, potential threats for salmon farming were found within the microbiota, including fish bacterial pathogens, virulence factors and antibiotic resistance genes.