Contamination of aquatic systems mainly by urbanization and poor sanitation, deficient or lack of wastewater treatments, dumping of solid residues, and run off has led to the presence of particles, including manmade polymers, in tissues of many marine and freshwater species. In this study, the prevalence of microplastics (MPs) in freshwater fish from farmed and natural sources was investigated. Oreochromis niloticus from aquaculture farms in the Huila region in Colombia, and two local species (Prochilodus magdalenae and Pimelodus grosskopfii), naturally present in surface waters were sampled. Of the particles identified, fragments were the predominant type in the three tissue types (stomach, gill, and flesh) derived from farmed and natural fishes. MicroFT-IR spectroscopy was conducted on 208 randomly selected samples, with 22% of particles identified as MPs based on spectra with a match rate ≥ 70%. A total of 53% of identified particles corresponded to cellophane/cellulose, the most abundant particle found in all fish. Not all fish contained MPs: 44% of Oreochromis farmed fish contained MPs, while 75% of natural source fish contained MPs in any of its tissues. Overall, polyethylene terephthalate (PET), polyester (PES), and polyethylene (PE) were the prevalent MPs found in the freshwater fish. A broader variety of polymer types was observed in farmed fish. The edible flesh part of fish presented the lower prevalence of MPs compared to gill and stomach (gut), with gut displaying a higher frequency and diversity of MPs. This preliminary study suggests that the incidence and type of MPs varies in farmed verses natural fish sources as well as across different tissue types, with significantly less detected within the edible flesh tissues compared with stomach and gill tissues.