Ancient DNA research has focused on the genetic patterns of the earliest farmers during the European Neolithic, especially with regards to the demographic changes in the transition from hunting and gathering to agriculture. However, genetic data is relatively lacking after this earliest transition period, when societies had fully adapted to new agrarian lifestyles specific to their local environment. During the later central European Neolithic (ca. 3600–2800 cal BC), large-scale collective burials and monumental architecture appeared within the landscape of many agricultural societies. This phenomenon has been argued to represent the emergence of a “collective” identity. With the aim of exploring genetic-based relations among individuals collectively buried, we obtained human skeletal remains of nearly 200 individuals from four later Neolithic collective burial sites in Germany: Calden, Odagsen, Groβenrode, and Panker. We successfully reproduced reliable mitochondrial DNA (mtDNA) haplotypes from eight Neolithic individuals, which were assigned to haplogroups H, HV0, and X2. Shared haplotypes observed among individuals within Calden and Odagsen suggest that genetic relations may have shaped the arrangement of the deceased within later Neolithic agricultural groups.