In Bangladesh from 1 July to 30 September 2010 there were 104 animal cases of anthrax and 607 associated human cases. This investigation was conducted in Sirajganj district in December 2010, on eight farms where animal cases had occurred. Bacillus anthracis was recovered from soil samples and turbinate bones on six farms. Canonical single nucleotide polymorphism (SNP) analysis showed that all the isolates belonged to the major lineage A, sublineage A.Br.001/002 of China and South East Asia while a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) with 15 VNTRs demonstrated three unique genotypes. The single nucleotide repeat (SNR) analyses showed two SNR types in 97 out of 99 isolates; nevertheless, due to its higher discriminatory power the presence of two isolates with different SNR-type polymorphisms were detected within two MLVA genotypes. The epidemic occurred during the monsoon season, a time of extensive flooding, suggesting that the source was contaminated feed, not grazing, which is supported by the genetic variance.