Endemic plague in Madagascar is perpetuated by a reservoir cycle made up of Rattus rattus (the black rat) and multiple flea vector species, including the endemic ectoparasite flea, Synopsyllus fonquerniei, who’s annual cycle is strongly linked to the annual high transmission cycle of flea-transmitted plague. While previous studies have explored the genetic structure of R. rattus at large regional scales, the genetic concordance of host and parasitic flea has not yet been explored. We used microsatellite markers to determine the genetic structure of both species across local scales (40km by 40km) and to estimate the level of concordance in population genetic structure between these two species. We collected paired samples across 24 rural village and forest sites within the plague zone of the Central Highlands of Madagascar. 

R. rattus showed no structure at the levels tested, while S. foqnuerniei displayed weak isolation-by-distance patterns structured around forest connectivity, indicating less movement than their rat hosts. We suggest that the patterns found point to S. fonquerniei using their R. rattus hosts as transport through forests between rural villages, highlighting pinch points for plague spread. These findings have important implications for future mitigation strategies for bubonic plague, as well as highlighting the importance of exploring the relationship between host and  ectoparasitic vector genetic structure for host-vector systems.