Aquaculture of the sea cucumber Apostichopus japonicus has emerged as a pivotal industry in northern China in the early 21st century. It is estimated that the cultivation area for this species spans 250,356 ha, yielding an annual production of 248,508 tons. The swift growth and intensification of sea cucumber farming practices have triggered a spectrum of diseases, resulting in significant economic detriment. This study offers an exhaustive account of a particular ciliate species, identified through smear and histopathological observations, hematoxylin-eosin staining, scanning electron microscopy, and molecular biology techniques, detailing its morphology, size, cellular architecture, and reproductive mode. The ciliate exhibits a torch-like shape, measuring 40–82 μm in length and 12–35 μm in width. It is characterized by the presence of both a macronucleus and a micronucleus. The anterior end is slender and blunt, while the posterior end is the widest part of the organism. A peristomal disc (PD) is situated at the body's terminus, with the mouth positioned centrally on the PD and a lip-like projection (6–10 μm in length) extending from one side. The organism's surface, particularly the area surrounding the oral region, is adorned with an abundance of long cilia. A single contractile vacuole is observable at the aboral end of the ciliate. It possesses 17–21 somatic kineties, complemented by 3 membranelles (M1, M2, M3) and a paroral membrane (PM) within the buccal cavity. One contractile vacuole was seen at the aboral end. There were 17–21 somatic kineties, while three membranes (M1, M2, M3) and a paroral membrane (PM) located within the buccal cavity. The first somatic kinety is notably more extended than the others, uniquely reaching a length of 10 μm around the PM. The PM, comprised of 2 somatic kineties in a “zig-zag” formation, follows a spiral path, making approximately 360-degree turns in conjunction with M1, M2, and M3, and culminates at the mouth depression. The ciliate reproduces through transverse binary fission or sexual conjugation. Based on these distinguishing features and molecular biological identification results, the ciliate is provisionally classified within the genus Boveria, as Boveria labialis. Histopathological examination has shown that these ciliates are predominantly found within the respiratory trees of their hosts, where they inflict damage to the epithelial tissues. This damage manifests as cell necrosis, structural disintegration, and the shedding of cells from the respiratory tree's epithelial lining. In severe cases, the affected respiratory tree and other viscera may be expelled. Epidemiological studies have indicated that infected individuals do not present with any overt external lesions. The findings of this research are instrumental for the management of diseases and the promotion of health within the sea cucumber aquaculture industry.