Secretory proteins play an important role in the process of molecular interaction between pathogen and host plants. In this paper, we employed SignalP 3.0, TargetP 1.1, KohGPI and TMHMM 2.0 to predict the secretory proteins of root-knot nematode and finally we got 2 622 and 1 696 secretory proteins for Meloidogyne incognita and Meloidogyne hapla respectively, correspondingly accounted for 13.65% and 12.95% of the total proteins. 754 and 466 secretory proteins from Meloidogyne incognita and Meloidogyne hapla respectively showed homology to proteins in KOG (eukaryotic orthologous groups) database with blastp (E <1e-10) The main functions of those homologous proteins in KOG database were related to energy metabolism, transport, signal transduction and regulation of transcriptional activity. GO(gene ontology) analysis showed that M. incognita and M. hapla differed significantly in the number of secretory proteins for nuclear localization signal and transcription regulator activity. Finally, 54 motifs were found to be shared by the signal peptides of M. incognita and M. hapla using MEME / MAST.