ABSTRACT Ciliate protozoa are highly contagious pathogens causing significant economic losses in global finfish aquaculture. While conventional chemotherapeutics like formalin offer control, their overuse raises environmental and safety concerns, creating an urgent need for sustainable alternatives. This review systematically synthesizes research from the past two decades, evaluating the antiparasitic efficacy of 29 medicinal plants against major ciliate pathogens such as Ichthyophthirius multifiliis and Cryptocaryon irritans . The analysis reveals that numerous plants, particularly Sophora flavescens , Cynanchum atratum , and Curcuma longa , exhibit exceptional efficacy. Their bioactive compounds, including alkaloids, flavonoids, and tannins, effectively eliminate parasites by disrupting cell membranes and metabolic pathways, often with substantial safety margins compared to chemical drugs. Despite this potential, significant barriers hinder their practical application. These include a scarcity of large‐scale field trials, a lack of standardized formulations leading to inconsistent results, and complex, divergent regulatory hurdles that impede commercialization. This review concludes that while medicinal plants are a highly promising tool for sustainable aquaculture, realizing their full potential requires a concerted effort to bridge the gap between laboratory research and practical, regulated application through field validation and standardized product development.