Whether encoding protein is the golden standard for distinguishing protein coding genes and non-coding RNA (ncRNA), while recent detected peptide coding small open reading frames (sORFs) from lncRNA challenged this standard. Now, more and more studies have shown that peptide coding sORFs exist in different regions of eukaryotic genomes universally, which play important roles in biological activities. Because of the low expression level as well as low abundance and the short sequence length, there are few computational and experimental methods or data resources exploited for peptide coding sORFs, then study of peptide coding sORFs is in its early phase. At present, most studies of peptide coding sORFs are concentrated on several model eukaryotes，people know little about its intrinsic features, therefore the peptide coding sORFs bring more challenges for genome annotation under the precision medicine era. In this work, comprehensive sequence and function analysis of the peptide coding sORFs were firstly performed based on more than 80 prokaryotic genomes. The results show that peptide coding sORFs also exist in prokaryotic genomes universally and many peptide coding sORFs sequences are conserved among different genomes. Further analysis indicates that the sequence complexity decreases and their functions are relatively centered with the decrease of sequence length of peptide coding sORFs. Finally, we summarized the problems and challenges psoposed by peptide coding sORFs, which will provide solid theoretical basis for future sORFs related studies.