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Although a variety of hierarchical image segmentation procedures for remote sensing imagery have been published, none of them specifically integrates remote sensing time series in spatial or hierarchical segmentation concepts. However, this integration is important for the analysis of ecosystems which are hierarchical in nature, with different ecological processes occurring at different spatial and temporal scales. Therefore, the objective of this paper is to introduce a multi-temporal hierarchical image segmentation (MTHIS) methodology to generate a hierarchical set of segments based on spatial similarity of remote sensing time series. MTHIS employs the similarity of the fast Fourier transform (FFT) components of multi-seasonal time series to group pixels with similar temporal behavior into hierarchical segments at different scales. Use of the FFT allows the distinction between noise and vegetation related signals and increases the computational efficiency. The MTHIS methodology is demonstrated on the area of South Africa in an MTHIS protocol for Normalized Difference Vegetation Index (NDVI) time series. Firstly, the FFT components that express the major spatio-temporal variation in the NDVI time series, the average and annual term, are selected and the segmentation is performed based on these components. Secondly, the results are visualized by means of a boundary stability image that confirms the accuracy of the algorithm to spatially group pixels at different scale levels. Finally, the segmentation optimum is determined based on discrepancy measures which illustrate the correspondence of the applied MTHIS output with landcover-landuse maps describing the actual vegetation. In future research, MTHIS can be used to analyze the spatial and hierarchical structure of any type of remote sensing time series and their relation to ecosystem processes.