Landscape characteristics influence both vector and host habitats affecting the spatial and temporal distribution of vector-borne diseases. Anaplasma phagocytophilum is one of the most widespread tick-borne diseases in Europe causing tick-borne fever (TBF) in domestic ruminants, and granulocytic anaplasmosis in humans, horses and companion animals. The aim of this study was to identify landscape factors associated with Equine Granulocytic Anaplasmosis (EGA) cases in a refined temporal and spatial analysis by combining land cover data and presence/absence disease data, using a geographical information system (GIS). This study is a retrospective analysis utilizing 1030 EGA diagnostic test results extracted from the National Veterinary Institute (SVA, Sweden). The association between EGA and different land cover types was analyzed with generalized linear models. To analyze the relation between landscape heterogeneity and EGA, we calculated the Gini-Simpson index. Our results showed a significant increase in the proportion positive EGA cases from 2002 to 2015 and marked differences in the seasonal within year distribution of EGA cases. The association with landscape configuration is shown by the positive relationship between A. phagocytophilum and coniferous forest, water bodies, and landscape heterogeneity, respectively. The information on the eco-epidemiological drivers for EGA can be central for disease control and prevention. Our method of linking land cover to disease risk may be applied to other vector-borne diseases and to other study regions.