BackgroundOur investigation focused into Labeo rohita, commonly known as Rui, a freshwater aquatic species in Bangladesh. Despite their nutritional significance, these fish faced a pressing challenge: parasite infections threaten the economic stability of the aquaculture sector.ObjectivesThe present study aimed to investigate the parasite and histological changes in major organs of L. rohita, collected from Khulna region – Dumuria, Paikgacha and Rupsha.MethodsAbout 180 (30/month) specimens were collected between the month of March and August 2023 to observe the parasitic status in L. rohita.ResultsThrough microscopic examination, a total of 323 parasites were uncovered, spanning categories including Cestode, Nematode, Acanthocephala, Trematode and Digenia, predominantly residing in the intestines of L. rohita. The highest prevalence rate (70%) was recorded in both March and May 2023, with peak mean intensity observed in July (3.73). Notably, the highest mean abundance (2.37) exhibited in July and index of infestation (45.34) in June. Histological analysis confirmed parasitic infestations in the gastrointestinal region, with displaying histological changes within major organs such as the liver, kidney, gills, spleen and testicles due to parasitic infection.ConclusionThis study concluded that the indentified six categories of parasite and the affect of parasitic infestation in major organs of L. rohita within the study period. Urgent efforts to implement effective strategies for controlling the parasite infections in aquaculture to ensure the sustainable production of this invaluable fish species.