The occurrence, state and differences of species that might be harmful for green areas users were evaluated along the urban gradient (town of Č. Budějovice, The Czech Republic). Species samples were selected from vascular plants (tree and shrub species, herbs), invertebrates (ticks, aphids), mammals (vertebrates and/or rodents), fungi (primary toxic and secondary harmful species). Several results were pointed out by the authors for the area planning and management. (1) More than 379 plant species of the town is potentially hospitable for some of 17 pest aphid species impacting economically important plantations. The local management of plant inhospitability is possible via the plant assemblages composition. (2) The small and middle-size mammals survive or penetrate from suburb to the residential and housing centres themselves. The solution bears on the skilled green area user and control of pest outbreaks in any area. (3) About 30 primary toxic mushroom species were recorded in areas with new block of flats, suburban periphery and industrial area. The solution bears on the skilled green area user; fungi management is not recommended. (4) The individual plant species might be re-evaluated in a sense of their roles under social consensus of their harmfulness, utility and management at the date. (5) The standardization of the species data to management and planning is possible via smaller units of the town environment, i.e., on hierarchical levels of important individual organisms and their habitats. The GIS developed by municipality administration is powerful instrument of sharing the data about habitats / organisms between all to whom the data may concern.