The present paper aims to investigate the distribution of two peptide: N­-glycanase (PNGase) genes in Elizabethkingia meningosepticum (EM). The genomic DNAs of 65 clinical strains isolated from 3 hospitals in Zhejiang Province were extracted and subjected to polymerase chain reaction (PCR) for 16S rRNA, PNGase F and PNGase F­-Ⅱ genes respectively. The PCR products were sequenced and compared to the known sequences in National Center of Biotechnology Information (NCBI). The results showed that the positive rate of PNGase gene was 98.5% and the PNGase F/PNGase F­-Ⅱ gene co­existence rate was 60.0%. The positive rates of PNGase F gene and PNGase F­-Ⅱ gene were 63.1% and 95.4%, respectively (matching χ² test, P<0.01). The results indicate that the developed PCR can be used to detect PNGase gene in EM strains and PNGase activity may be crucial for the survival.