The use of plants for herbal medicine in the Indonesian aquaculture is still poorly known. The present study aimed to provide an inventory of the plants used by fish farmers, establishing their respective ethnobotanic importance and identifying the variables that determine the use and the choice of these plants in fish health management. A survey based on a semi-directive questionnaire was conducted using a representative sample of fish farmers (n = 504 from 176 villages) from the province of West Java. Of these fish farmers, 46% [41%, 50%; CI95%] of them use plants in their farms and 79 species of plants belonging to 36 families have been identified. Most of these plants were common plants used also traditionally in human pharmacopeia. Four categories of plant use were identified namely: improvement of water quality; reduction of fish stress; increase of fish resistance to pathogens; and treatment of fish diseases (when an outbreak occurred). In order to appraise the significance of plant usage, the following ethnobotanic parameters were determined: the Use Value (UV), the Fidelity Level (FL) and the Informant Consensus Factor (ICF). The Use Value (UV) was generally low for plants except for Carica papaya which reached the highest UV scores. The majority of the plants were used according to personal experience of the fish farmers and the knowledge related to herbal therapy appeared variable among fish farmers. Only 26 species of plants had a UV > 0.025. The highest Fidelity Level (FL) value was obtained for C. papaya. The Informant Consensus Factor (ICF) of each plant usage was relatively high for all four categories of use - ranging from 0.78 to 0.88 - but the same plant may have several therapeutic indications. The use of plants, as well as their variety and number, depended not only on fish species, production systems and production areas but also on social characteristics such as the professional experience of fish farmers and their ethnic origin. To our knowledge, this is the first ethnobotanic survey specifically applied to aquaculture. It was able to identify the species of plants used in the West Java Province, and how they are used. It also highlighted the significance of traditional Indonesian herbal therapy in aquaculture. The use of several plants in aquaculture is reported for the first time in this study.