Understanding the mechanism shaping species assemblage is a fundamental goal in ecology. In the past two hypotheses have been suggested. One is the filtering hypothesis where environmental factors select for species of similar traits such that they co-occurring in similar niches. The other is the competitive exclusion hypothesis where related species are driven far apart by competition such that they over-disperse across different niches. Here, we investigate the relationship between species assemblage and their phylogenetic relatedness from the network perspective by using five different ecosystems ranging from oceans to an inland lake. We quantified the similarity in species’network positions in a food web and cluster them into different trophic role groups; and from an on-line database we quantified their phylogenetic distances. We then investigated whether related species tend to under or overdisperse across different trophic role groups. In general, our result suggests the environmental filtering process is the dominant force shaping the species assemblage of those ecosystems. However, there are some possible cases where related species are driven by competition such that they evolve to adopt different trophic roles in relatively closed ecosystems.