The development of tree inventories and open data bases provides green space managers a better understanding of tree morphological diversity in urban areas. However, studies on tree genetic diversity in cities remain rare. The aim of our study is to provide better knowledge on tree intra- and interspecific diversity to improve tree management in urban areas. We characterized 83 individuals of Tilia species and clones in streets and parks in Paris (France) based on both morphological characters (leaves, fruits and twigs) and genetic profiling by using nuclear microsatellite markers. We found five species through morphological identification: Tilia cordata, Tilia dasystyla, Tilia xeuchlora, Tilia xeuropaea and Tilia platyphyllos. Analysis of genetic profiles allowed to distinguish three genetic groups correlated to T. cordata, T. xeuchlora and T. platyphyllos. Tilia xeuchlora had the largest number of the same clonal profile (20 individuals out of 36) in Paris while no clone was found in T. platyphyllos group. In some cases, clones were planted in the same street for aesthetic purposes. This can increase disease risk and diminish resilience to climate change. Knowledge on genetic variability between and within species is essential to hedge those risks and for evaluating individual responses to environmental conditions. Our study shows that production and purchasing practices by green space managers need new insights and that tree nurseries can play a crucial role in supplying trees with diverse genetics. Green space managers can reinforce diversity where possible in some areas (development of urban forests, greening of secondary streets or sidewalks, etc.) to improve ecosystem services in urban areas.