Cell-to-cell communication via peptides is recognized as an essential process of plant development. The plant CLAVATA3/EMBRYO SURROUNDING REGION (ESR)-related (CLE) peptides, a group of small secreted peptides derived from the C-terminal region of preproproteins, control the balance between cell proliferation and differentiation in plant development. CLAVATA3 (CLV3) is one of the best-characterized CLE peptides and functions in stem cell niche maintenance in shoot apical meristems (SAMs) through the leucine-rich repeat receptor-like kinases (LRR-RLKs). Recent studies have shown that CLE peptides are involved in the response to phosphate and in the autoregulation of nodulation. These findings demonstrate that, along with the well-known role for CLV3 peptide signaling in meristem maintenance, CLE peptide signaling is also utilized in different developmental processes and environmental responses. In this review, we summarize current knowledge about the functions of CLE peptides in plant development and environmental responses.