Benthic algae are important indicators for ecological conditions of streams and rivers, but studies on effects of urbanization on benthic algal diversity is still sparse. In this study, we surveyed 74 sites from nine rivers located in Shenzhen City in the wet and dry season of 2020, and compared differences of α- and β- diversity of lotic benthic algal assemblages between urban and suburban groups. A total of 301 algal taxa were identified in the two seasons, among which the most taxa belonging to diatoms. The relative abundance of pollution indicator species such as Nitzschia palea, Navicula cryptocephala and Nitzschia inconspicua was higher in the urban groups, while the suburban groups with higher relative abundance of Achnanthidium minutissimum, which is an indicator species of clean water. We found that urbanization had no significant effects on algal α-diversity indices including richness, Shannon-Wiener's diversity index, and Pielou's index; while, algal community compositions in urban sites were significantly different from that of suburban sites. β-diversity of benthic algae, represented by centroids of the principal coordinate analysis, was lower for the urban sites than that of the suburban sites, with more significant difference in the dry season. The difference of benthic algal assemblages between the two groups mainly came from species turnover components. Total nitrogen, COD_Mn, conductivity, pH, turbidity and water depth were identified by the Mantel test as the environmental factors that were significantly correlated with algal community compositions in the urban group; while, TN, Dissolved inorganic Phosphorus (PO₄-P) and conductivity were significantly correlated with the community compositions of benthic algae in the suburban group. We found that levels of TN, PO₄-P, COD_Mn and conductivity were significantly increased in the urban group, which decreased β-diversity of benthic algae communities in Shenzhen rivers. To protect biodiversity of Shenzhen rivers, we therefore suggest to effectively control domestic and industrial sewage in urban areas to reduce human disturbance to rivers.