Heat shock transcription factor 1 (HSF1) is an important activator of innate immunity in the response of invertebrates to pathogen invasion. In the present study, a HSF1 was characterized in Pacific oyster Magallana gigas (MgHSF1), and its association of single nucleotide polymorphisms with susceptibility/resistance of oyster to Halomonas sp. 7T were investigated. MgHSF1 shared highly conserved DNA binding and acetylation sites with other organisms. The MgHSF1 mRNA showed high expression in haemocytes, and was significantly induced by lipopolysaccharide stimulation. The single nucleotide polymorphisms (SNPs) within promoter region of MgHSF1 gene from two oyster populations (the bacterial-resistant population and the common population) were investigated to analyze their association with bacterial resistance. Nine out of 14 SNPs including -543 A/G, -494 C/T, -488 T/A, -476 G/A, -336 C/T, -335 T/C, -334 C/T, -307 T/C and -268 T/C were found to be associated with bacterial resistance. Moreover, haplotypes TCTCGA was associated with bacterial resistance. The results threw lights on the molecular mechanisms of different oyster populations' resistance to bacterial diseases which suggested that the increased bacterial resistance of bacterial-resistant population was associated with the higher expression of MgHSF1. Meanwhile, the nine genotypes (-543 G/G, -494 T/T, -488 A/A, -476 A/A, -336 T/T, -335 C/C, -334 T/T, -307 T/T, and -268 C/C) and one haplotype (TCTCGA) could be used as potential markers for oyster selection breeding with higher bacterial resistance.