Prodigiosin (PG) is a red pigment mainly biosynthesized by Serratia marcescens. This pigment compound possesses potential applications in various fields. Due to showing various bioactivities, PG has received much attention for study. Numerous review papers concerning the production and applications of PG were reported. However, almost all previous reviews focus on its potential application in medicine. To date, PG has been widely investigated for its application in agriculture with plant anti-pathogenic potent against nematodes, fungi, and bacteria. To highlight the novel and promising utilization of PG in agriculture, this review extensively presented and discussed the applications of PG in agriculture via in vitro tests, greenhouse tests, and field studies. The mechanism action of PG was also presented in this paper.