Myxobolus Bütschli, 1882 is a highly important genus of fish myxozoans, consisting of many species that cause serious diseases in ornamental cyprinid fish species in different geographic areas by infecting a wide range of organs. This study describes a new Myxobolus species infecting the gill lamellae, gill rakers and skin epidermis of goldfish (Carassius auratus) from Mohammadshahr, Iran, based on detailed morphological, histological and molecular analysis. Mature spores were small and spherical in shape, consisting of two symmetrical shell valves in frontal view, measuring 10.3 (9.8-10.9) μm in length and 10.5 (10.3-11.2) μm in width. Two equal-sized relatively pyriform polar capsules were 5.4 (3.9-6.0) μm long and 4.5 (3.7-5.2) μm wide. The polar tubules were coiled with 4-6 turns. A comparative analysis of the morphological and molecular data confirmed that this species is distinct from other identified myxosporeans. Plasmodia in the cutaneous tissue were found in the epidermis, causing extensive hyperplasia of Malpighian cells and mild inflammatory infiltration. In the gill tissue, plasmodia affected only one side of the lamellae, leading to hyperplasia of the lamellar epithelium, edema, and lymphoplasmacytic branchitis. A novel myxozoan species, Myxobolus branchioepidermis n. sp., has been proposed. The study provides a comprehensive analysis of the morphological, histological, and molecular characteristics of this parasite, which infects the gill lamellae and epidermal layer of the skin in oranda goldfish (C. auratus). The identification of this new species adds to the growing body of research on myxozoan parasites and highlights its potential impact on ornamental fish aquaculture.