Accumulated evidence suggests that peptides play diverse roles in various aspects of plant growth and development. Therefore, many research groups have developed and utilized new methods for the identification of peptides in different organisms. Nevertheless, the number and diversity of identified peptides remain lower than expected. In addition, the number of identified peptides is underestimated because of their low endogenous concentrations and, consequently, technical difficulties with their isolation. Additionally, while some types of peptides undergo functional maturation via proteolytic processing or post-translational modifications, which are important for their biological activity, most of the enzymes involved in the maturation of peptides have not yet been identified. Together, these factors indicate that the investigation of peptides is in its beginning stages in plants, as in other organisms. This review summarizes the biosynthesis mechanisms, identification tools, post-translational modifications, and biological functions of plant peptides, and the importance of post-translational modifications in peptide activity.