Parasitic infestations are one of the most concerning problems limiting ornamental fish farming. In addition to the direct economic losses due to the major mortalities, parasites may significantly negatively impact the body shape, coloration, growth rate, and health condition of the fish. The results of the study highlight the importance of comprehensive parasitological analysis in the diagnosis and treatment of parasitic infections in ornamental fish farms. The presence of multiple parasites in the affected fish emphasizes the need for effective biosecurity measures, such as extending the quarantine period for newly imported fish, closely monitoring fish populations, and implementing isolation units to prevent the spread of infections. By implementing these preventative measures, ornamental fish farmers can reduce the risk of parasitic infections and ensure the health and well-being of their fish populations. This, in turn, can lead to increased profitability and sustainability for their business. Overall, the current study aimed to conduct a clinical, histopathological, and phylogenetic analysis of the epibiont ciliated protozoan Epistylis wuhanensis and the copepod crustacean Lernaea cyprinacea in a freshwater ornamental fish farm in Iran. Furthermore, it provides valuable insights into the prevalence and impact of parasitic infections in ornamental fish farms and underscores the need for continued research and the development of effective preventative measures to address this issue. A total of 60 symptomatic freshwater ornamental fish, including 30 guppy (Poecilia reticulata) and 30 sailfin molly (Poecilia latipinna), were packed in polyethylene bags filled with oxygenated pond water and transported to the Ornamental Fish Clinic, Faculty of Veterinary Medicine, University of Tehran, for parasitological analysis. Following the clinical examination, histopathological analysis was performed on 10% NBF (neutral buffered formalin)-fixed samples from affected tissues, including the skin, skeletal muscle, and liver, to identify any pathological changes associated with the parasitic infections. Furthermore, the DNA was extracted from the 99% ethanol-fixed samples using a commercial DNA extraction tissue kit (SinaPure DNA, Iran), and PCR was performed using Peri18S-F1 (5′-ACC TGG TTG ATC CTG CCA GT-3′) and Peri18S-R1 (5′-TGC AGG TTC ACC TAC GGA AA-3′) (first reaction), and Peri18S-F2 (5′-CCG CGG TAA TTC CAG CTC-3′) and Peri18S-R2 (5′-GAT CCC CTA ACT TTC GTT CTT GA-3′) (second round) primers for the identified parasites. Finally, the PCR products were sequenced using Sanger dideoxy sequencing methods, and the resulting sequences were compared to sequences in the BLAST search program to provide a comprehensive picture of the current parasite-based disorder. The crustacean L. cyprinacea and the epibiont sessilid E. wuhanensis were identified in the examined ornamental guppy (6/30) and sailfin molly (6/30), with an overall parasitic prevalence of 20.00% (12/60). Ciliates were found in all tissue lesions but not in fish without lesions. A great number of the ciliated protozoan E. wuhanensis were found attached to the integumentary area of L. cyprinacea. Microscopically, oval to round granulomatous lesions were observed in cutaneous and skeletal muscles. Lymphoplasmacytic dermatitis and myositis were also observed. The crustacean L. cyprinacea serves as a mechanical vector for E. wuhanensis infection and spreads the disease in ornamental fish farming operations. For the first time in Iran, we successfully presented diagnostic morphological and molecular data on sessilids isolated from L. cyprinacea. Based on the findings of the current study, such parasitic infections may cause significant economic losses following invasion of the integument area of fish, eventually leading to death, if treatment is neglected or inadequate. Furthermore, the findings of the analysis were used to develop effective diagnostic approaches for the affected fish, as well as recommendations for improved health conditions to prevent future outbreaks of parasitic infections. However, further research is needed to determine the precise mechanisms of crustacean attachment and host-crustacean-peritrich protozoan interactions. Furthermore, the direct and indirect effects of various environmental factors on the emergence and spread of the current disease should be considered.