Innate immunity plays a vital role in protecting plants and animals from pathogen infections. Immunity varies with age in both animals and plants. However, little is known about the ontogeny of plant innate immunity during seedling development. We report here that the Arabidopsis (Arabidopsis thaliana) microRNA miR172b regulates the transcription of the immune receptor gene FLAGELLIN-SENSING2 (FLS2) through TARGET OF EAT1 (TOE1) and TOE2, which directly bind to the FLS2 promoter and inhibit its activity. The level of miR172b is very low in the early stage of seedling development but increases over time, which results in decreased TOE1/2 protein accumulation and, consequently, increased FLS2 transcription and the ontogeny of FLS2-mediated immunity during seedling development. Our study reveals a role for the miR172b-TOE1/2 module in regulating plant innate immunity and elucidates a regulatory mechanism underlying the ontogeny of plant innate immunity.