Resumo. Abstract Aim This study aimed to investigate the community structure of Zygnematophyceae algae in the periphyton of nine shallow urban eutrophic ponds from central Brazil. Additionally, we compared two different substrates, hypothesizing that community structure attributes (chlorophyll a; Zygnematophyceae density, composition and richness) would differ between them. Methods Samples were carried out in August 2014. Periphyton was collected from two different substrates, macrophyte (epiphyton) and rocks (epilithon). Results The ponds presented pH ranging from neutral to slightly acidic and electrical conductivity in general higher than 60 µS.cm-1. Zygnematophyceae contributed with 0.82% of total periphyton community density in the epiphyton and 0.02% in the epilithon. Altogether 49 Zygnematophyceae taxa were recorded, distributed in 13 genera. Based on frequency of occurrence, most taxa were classified as rare, being present in less than 25% of the ponds. The taxa with higher densities were Cosmarium regnesii var. regnesii, Cosmarium abbreviatum var. minus, and Mougeotia sp. 3. When each pond was considered individually, other taxa were highlighted as the most abundant among Zygnematophyceae. It was the case of Staurastrum smithii, Cosmarium exiguum, Mougeotia sp. 1 and Mougeotia sp. 2. The two ponds with highest Zygnematophyceae density showed high similarity in the species composition (>70%); however, among the others, it was relatively low (<50%). Conclusions The eutrophic ponds considered in this study presented high periphytic biomass, but with low Zygnematophyceae representativeness. The periphyton attributes were not significantly different between macrophytes and rocks. The substrate type was not a determinant factor for Zygnematophyceae periphytic algae in the studied ponds.