Rhipicephalus microplus, is an invasive tick species associated with the highest economic losses where it occurs. Invasion of West Africa, where breeding is in 95% of case with low input, started in 2000s and was followed by breeder's complaints of acaricide resistance. Since understanding of population structure could help tick control, this study aimed to investigate processes which influence R. microplus invasion in Benin and Burkina Faso. Thus, seven microsatellites (SSRs) markers were applied to analyse 436 ticks from Benin and Burkina Faso. Subsequently, determination of population limits, population size, and investigation on isolation by distance pattern were achieved. Analyses revealed that herd is the relevant level of population limit in Benin and with the whole dataset. Significant differentiation was highlighted between herds and between R. microplus population from Benin and Burkina Faso. Migration occurred between herds, as indicated by assignment results and migration rates. Furthermore, any bottleneck was not evidenced within dataset. Results suggested that the origin of R. microplus population of Burkina Faso could be Côte d'Ivoire. The limit of population being the herd has obviously to be considered in tick control strategies. Thus, to be efficient, tick control programs should primarily focus on the cattle coming back north after transhumance.