Efforts to reduce human-wildlife-conflict are integral to wildlife management and conservation in urban habitats. In our study, we identified the HWC situations in urban areas of Krakow city, based on animal-vehicle collisions, intrusion to property, and damages. Hot spot analysis and Moran’s Index were used to identify the location of maximum potential conflict. We analysed 2512 incidents in which animals (of which 85% included mammals and 15% birds) were involved in conflict situations between 2007 and 2013. A significant seasonal variation was observed among the animals. We also identified roe deer (50.23%), red fox (22.80%) and wild boar (11.40%), as the three prominent conflicted animals. Getis–Ord Gi* analysis was used to identify spatial clusters of conflict. A significant spatial association was found in the location of clusters of hot spots in specific land-use based on Moran’s Index. Hot spots of roe deer and wild boar were high in grasslands and in forest and for red fox in built-up area. The results underscore the notion that conservation and wildlife management efforts must take into account differences in the seasonality of HWC among species. This information can be used to inform mitigation strategies.