Abstract: Paralogs and orthologs are two main types of the homologous sequences originated during speciation and genome evolution.Although methods of ortholog identification across species have been develo-ped,the method or parameters for paralog prediction are still uncertain especially for solanaceous species.Now whole genome sequencing of tomato is under going,parameters for paralog prediction are needed to study the evolution of tomato genome.After self-blasting of tomato BAC DNA sequences downloaded from GenBank,here we determined that E-value≤10^-40,HSPs length≥200 bp,sequence identity≥80% are the appropriate parameters or combination of parameters.