Macrophage migration inhibitory factor (MIF) is an ancient cytokine that engages in innate immune system of vertebrates and invertebrates. In this study, the MIF gene homologue (PmMIF) was cloned from the black tiger shrimp, Penaeus monodon. The full-length cDNA sequence of PmMIF was 838 bp and contained 78 bp 5′ untranslated region (UTR) and 397 bp 3′ UTR, and an open reading frame (ORF) of 363 bp which coded 120 amino acids (aa). Multiple alignment analysis showed that the deduced amino acid sequence shared 98% identities with MIF from closely related species of Litopenaeus vannamei. Quantitative real-time PCR (qRT-PCR) analysis indicated that PmMIF was highly expression observed in hepatotpancreas and gills. After Vibrio harveyi challenge, PmMIF mRNA level in hepatopancreas and gills were sharply up-regulated at 6 h post-injection, and reached the maximum at 12 h. PmMIF expression level in the hepatopancreas and gills were up-regulated markedly under low (2.3%) and high (4.3%) salinity exposure, respectively. PmMIF expression level in gills increased significantly at 12 h and reached peak values (2.5- fold, 6.4-fold and 1.8-fold compared with the control) at 12 h, 48 h and 12 h after zinc, cadmium and copper exposure, respectively. In the hepatopancreas, the expression of PmMIF reached maximum levels (8.5- fold, 6.2-fold and 2.1-fold compared with the control) at 24 h, 6 h and 48 h after zinc, cadmium and copper exposure, respectively. All the results indicate that PmMIF plays an important role in responding in the innate immune system of shrimps.