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The debate on the Anthropocene has become passionate during the past few years. This is partly because social scientists and humanists have adapted the concept creatively for their own research, as well as criticized the dominant role of natural sciences in defining the Anthropocene. We claim that to achieve a new level of transdisciplinarity it is vital for the Anthropocene research to fully acknowledge the theoretical, methodological and practical issues involved. We argue that inevitable as well as fruitful antagonisms can be identified between different disciplines and practices of trans- and interdisciplinary research improved by learning from these experiences. Here we analyze three ideas to enhance future transdisciplinary communication. First, we shed light on the current condition of transdisciplinarity in Anthropocene research by examining the challenges in Earth System science. Second, we widen the view on Anthropocene research by defining four different disciplinarily oriented research approaches to the Anthropocene: geological, biological, social, and cultural Anthropocene. Third, we reflect on the future challenges of merging these approaches into a new transdisciplinary Anthropocene research.