Background Non-random associations within and among groups of social animals can provide valuable insight into the function of group living and the evolution of social behaviour. Damaraland mole-rats (Fukomys damarensis) demonstrate extremely high levels of reproductive skew, and dispersal is considered to be male-biased in onset and frequency, although asymmetry in dispersal distance is yet to be investigated. Dispersal may be positively correlated with increasing favourable environmental conditions, such as rainfall, however, the effects of ecological constraints on dispersal and colony fission–fusion dynamics have not previously been demonstrated on a spatial scale. Here we provide the first spatial population genetic study for this species. We investigated genetic structure in a population of Damaraland mole-rats from the southern Kalahari in South Africa over 3 years, combining observational dispersal data from mark-recapture with population genetic data to evaluate (1) sex-bias in frequency and distance of dispersal in this species, and (2) the effect of rainfall on fission–fusion dynamics of colonies. Results Our results demonstrate (1) that both males and females favour local dispersal but on rare occasions may disperse over distances greater than 400 m, (2) that males may disperse over greater distances than females, and (3) that males more frequently immigrate into established neighbouring colonies than females, who predominantly disperse by colony fission, i.e. multiple individuals “budding” from their native colony into a neighbouring territory, thereby establishing new colonies. Furthermore, our results demonstrate (4) elevated dispersal and colony fission in association with increased rainfall, supporting the hypothesis that rainfall may play a significant role in the maintenance and/or disruption of reproductive skew in Damaraland mole-rat populations. Conclusion This study represents the first fine-scale spatial population genetic study in Damaraland mole-rats, and provides relevant insights into colony fission–fusion dynamics in a social and cooperatively breeding species.