The species diversity in a region is investigated by the indices (species richness, evenness and biodiversity) and their common methods of measurement (evenness index: Simpson, Camargo and Smith & Wilson; biodiversity index: Shannon-Wiener, Brillouin and Simpson). It is important to know the suitable index and its measurement method to study species diversity. To analyze the efficiency of the indices and their methods and the relationship between them in this research, the migratory aquatic birds in Parishan wetland was studied as biodiversity is better understood for birds than for any other organisms. Results showed that species richness alone cannot be utilized to estimate the species diversity of the study area. On the other hand, there are dissimilarities between the trends of evenness and biodiversity indices. In order to measure evenness index, there was no difference between Simpson and Camargo methods and their correlation was significantly high but Smith & Wilson was unequal to them. In biodiversity index, there also was no difference between Shannon-Wiener and Brillouin methods with significantly high correlation but Simpson was unlike them. This research showed that the application of indices of species diversity and their methods of measurement should be employed due to the purpose of experiment.