Thousands of small open reading frames (smORFs, <100 aa) located on lncRNAs potentially might be translated into peptides or small proteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of smORFs across different plant taxa. For thousands of smORFs, we demonstrate remarkable conservation and significant purifying selection, indicative of their functionality. The expression of the lncRNAs and translation of the smORFs are validated by RNA-sequencing and proteomics, respectively.