Diversity of Bacillus species varies with eco-system in the red soil region. Initial results of the study show that Shannon diversity index and Simpson diversity index have the same trend: forestland > upland > paddy field > eroded land. The richness index and the evenness index of the species have a similar trend, that is, forestland is the highest and eroded land the lowest. Besides, the results also show that Shanon-Wiener index is more useful than Simpson index to distinguish differences.