MicroProteins are small proteins that contain only a single domain which is related to larger proteins and they often regulate their targets via direct interaction to form non-functional complexes or engaging the larger protein in a novel complex. Recently, miP1a and miP1b, two microProteins that contain a single B-BOX domain and a carboxy-terminal PF(V/L)FL motif, were identified as flowering repressor in Arabidopsis. They repress flowering through two major mechanisms: First, they can modulate CONSTANS (CO) activity by directly binding to CO via their B-BOX domain and secondly, can engage CO in a repressor complex through interaction with the TOPLESS (TPL) co-repressor protein. In order to identify other components involved in the miP1a/CO/TPL repressor complex, a forward genetic screen was performed with transgenic miPa1-OX seeds. Two potential candidates were identified by a mapping-based sequencing approach. One mutant with a splice site mutation in the histone demethlyase gene JUMONJI 14 (JMJ14), suggesting JMJ14 could be part of the microProtein complex. Here, we found that miP1a regulates methylation in the FLOWERING LOCUS T (FT) promoter region to inactivate FT expression in a JMJ14-dependent manner. Apart from DNA modification, RNA modification is another important mechanism to regulate gene expression, particularly the methylation of adenosine in the N6 position (m6 A) of RNA. A second mutant was identified with an amino acid change in the FIONA1 (FIO1) protein sequence. We report FIO1 as an m6 A RNA methyltransferase with potential methylation ability to deposit m6 A in RNA, in Arabidopsis thaliana. Depletion of FIO1, as in fiona1 mutants plants promotes floral transition and affects vegetative growth. We show that FIO1 might influence flowering by methylation of the flowering repressor FLOWERING LOCUS C (FLC) mRNA and affecting its stability. These findings and the characterization of the RNA methylase in Arabidopsis provide new insight into flowering regulation and determines the crucial roles of m6 A in plant development. In rice, overexpression the synthetic microProtein of the flowering regulator HEADING DATE1 (HD1) causes a significantly early flowering phenotype compared to wild type plants, under long day conditions. These findings show the potential of microProteins to serve as powerful tools for modulating crop traits. Apart from the regulation of flowering, microProteins play central roles in plant development. Using a combination of comparative genomics and heterologous synthetic misexpression, we identified a microProtein, called LITTLE NINJA (LNJ), that acts as a modulator of jasmonic acid (JA) signaling. Overexpression of LNJ reduces plant growth and enhances the production of side shoots (tiller) in Brachypodium, barley and rice. Taken together, microProteins may provide a valuable tool for the study of post-translational regulation and can be utilized in crop breeding to modulate traits design-based.