Abstract: Molecular techniques，such as denaturing gradient gel electrophoresis(DGGE)，16S rDNA clone library，and DNA microarray, reveal extraordinarily divers species in the natural environment．Most of these species are unculturable and cannot be characterized precisely．Empirical indices like Shanon and Simpson have been traditionally used to evaluate the diversity． These indices，however, have certain disadvantages because of their dependence on sample sizes. To overcome such disadvantages，three approaches have been developed，which include parametric estimation, nonparametric estimation，and phylogenetie diversity estimation． These methods when integrated with molecular techniques． can enhance accurate estimation of species richness and diversity，and allow rigorous comparisons of different communities