Verticillium dahliae colonizes the xylem vessels of susceptible host plants. Hence it can be expected that the distribution of the fungus as well as disease progress will be influenced by the anatomy of the xylem of that host. Here, we studied the spatial and temporal distribution of V. dahliae in relation to recovery from disease symptoms in young European ash (Fraxinus excelsior) and Norway maple (Acer platanoides) trees that differ in vascular anatomy. Quantifying the amount of V. dahliae DNA at different heights in the stem of inoculated trees at different time points after inoculation showed that, in the year of inoculation, the speed of colonization of these two species by V. dahliae was similar. Nevertheless, in the year after inoculation disease incidence and also quantities of V. dahliae detected in maple trees were significantly higher than in ash trees, suggesting that the xylem of ash trees is much less supportive for growth and survival of V. dahliae than that of maple trees. Moreover, in this second year V. dahliae could not be re-isolated from the wood of ash trees that had recovered from disease and was only rarely detected by PCR, only in xylem of the previous year and never in the current xylem. In contrast, V. dahliae easily was detected in the wood of diseased ash and maple trees. Furthermore, despite the presence of a layer of parenchyma cells between growth rings in ash trees, in symptomatic ash trees V. dahliae was present in the xylem of the new growth ring. We also observed that V. dahliae can move downward from the point of inoculation into the root collar, which possibly provides a way for infection of new growth rings by circumventing the physical barriers within the stem xylem.