We propose the use of nematode generic biomasses as weighting factors for calculation of nematode community indices. Three data sets were used to calculate the indices using guild-based weighting (i.e., fixed weighting of nematode guilds) and genus-based weighting (i.e., weighting based on the nematode generic biomasses). The genus-based weighting factors were quadratically correlated with guild-based weighting factors, but the genus-based weighting factors were highly variable within each nematode guild, indicating that important information was likely missing when guild-based weighting was used. Although variation patterns of in the indices in response to management practices and land use were often similar for the two weighting systems, they sometimes differed substantially, and the specific index values frequently differed depending on which weighting system was used. In addition, the absolute values of the indices were frequently found to be different between the two weighting systems. Based on the comparison of indices from the two systems, we found that the genus-based system was complementary rather than superior to the guild-based system. It was suggested that both weighting systems should be used for the calculation of the nematode community indices in a study in order to better distinguish the treatment effects.