Here we have attempted to systematically characterize the potential functions of the small peptides of the 99 phage genomes found in the Mediterranean waters. Despite the lack of homology among the majority of the genomes (75 of them are singletons) we found several conserved short peptides across several genomes (>4). These peptides might have several interesting properties such as signaling peptides and cell penetrating peptides. Such a framework can be extended to predict function of short peptides for such datasets like phages in the microbiome.