An increase in the emergence/reemergence of infectious diseases of human and his domestic animals has been observed in recent decades. Most of these diseases are zoonotic and imply often a vector for their transmission. At the same time, land use changes linked to agricultural intensification and/or climate change have modified or will modify the landscapes. The aim of this study was to better understand the mechanisms involved in the maintenance of tick-borne diseases, in order to identify key factors of changes in transmission dynamics. We assessed intrinsic traits of small mammals linked to prevalence of two tick-borne infectious agents of potential public or animal health concern: Anaplasma phagocytophilum and Borrelia burgdorferi s.l., taking into account seasonal and interannual variations. Small mammals were live-trapped using 24 standardized trap-lines in May-June and October 2012 and 2013. 6 plots were located in a large deciduous forest, 6 at forest-meadow ecotones, 6 at woodlot-meadow ecotones, and 6 at hedgerow-meadow ecotones. Those last 18 plots were disseminated either in an agricultural matrix constituted of mixed farming systems or in more intensive crop-oriented farming systems. This sampling scheme represented all the dominant landscapes of the area. Captured animals were euthanized and the infectious tick-borne pathogens were searched for in tissue samples by PCR. Out of the 607 animals tested for both infectious agents, 42 were positive to A. phagocytophilum and 26 were positive to B. burgdorferi s.l.. Significant variation was observed between years, with higher prevalence in the year with low animal abundance. Seasonal variation was also observed, with higher prevalence in autumn of both years. We also found a significant difference in the prevalence in the two dominant species. Wood mice, despite harboring more ticks, had lower prevalence than bank voles. The prevalence of these two tick-borne infectious agents varied in time, possibly in relation to population density. Our results suggest a different implication of host species as infectious disease reservoir or as tick population dynamics amplifier. Long-term changes in small mammal abundance and/or community structure caused by global changes (i.e. climate change and land use changes) can have drastic impact on tick-borne disease transmission. The conduct of long-term studies at the meta-community level (i.e. hosts and vectors) is recommended to anticipate changes in tick-borne diseases transmission and anticipate possible outbreaks