The distribution of divergence times among community members, which depends on species sampling patterns, is an important aspect of community phylogenetic structure. Nevertheless, the incorporation of information regarding divergence time distribution is lacking from current phylogenetic diversity measures. Community genetic diversity may be translated into an effective community size for a hypothetical community generated by random speciation, extinction, and species sampling. In this study, we formulated a new index of community diversity, the phylogenetic skew index. We analyzed its statistical behavior using data from a monthly-monitored fish community at nuclear reactor water intakes in northern Taiwan, and developed a correction method to compensate for small sample size bias. We also performed a Bayesian analysis of variance under a gamma distribution model to detect annual and seasonal variation patterns in phylogenetic skew in the fish community. We show that our new phylogenetic skew index provides additional information regarding community diversity.