An atoxigenic Aspergillus flavus strain AF051 collected from a peanut field in Jiangsu province, P. R. China was characterized by analysis of aflatoxin gene cluster in this study. By using a thermal asymmetric interlaced PCR (TAIL-PCR) and conventional PCR techniques, an 89.59-kb deletion was found in the cluster, and this deletion was replaced by a 3.83-kb insert, which was located at 300-bp upstream ver1 gene and 2594-bp downstream a putative gluconolactone oxidase gene. Based on the DNA sequence at the breakpoint, a nested-PCR method was developed for the rapid and sensitive detection of AF051 strain in soil and peanut samples once the strain is used as a biological agent.