Computer assisted molecular fragment evaluation (CAMFE) program has been established and applied to the data set analysis of the mutagenicity of 59 organophosphorus pesticides (OPPs) in Salmonella reversion assay. The results favour the hypothesis that the mutagenic properties of OPPs lie in their alkylation to DNA mainly by the molecular fragments containing methyl groups rather than those containing ethyl groups. Oxygen atom in phosphoryl group may prompt the mutagenic ability induced by OPPs; However, the mutagenic ability may be decreased by sulfur atom, the substitute of oxygen atom at the same site in PPs structure. It was suggested that, among the most relevant fragments, the methoxyphosphinyl group appears as the common structural subunit responsible for the activities detected in the Salmonella reversion assay, while the ethyl thionophosphinyl group appears as the descriptor of negative results.