The mixing of a passive tracer in the stratosphere and lower mesosphere is studied on the basis of the effective diffusivity, which is obtained in the framework of the tracer-based coordinate system. This characteristic is proportional to the average diffusion flux over Lagrangian contours and inversely proportional to the mean tracer gradient. The tracer distribution used in the calculation of the effective diffusivity is obtained after integration of the advection-diffusion equation using general circulation model winds and a new numerical advection scheme with small numerical diffusivity. Using some theoretical and experimental arguments, it is shown that the interpretation of the seasonal variability of the effective diffusivity field cannot be done on the basis of the momentary wind field alone, but some flow history should be taken into account. The climatology of the effective diffusivity for different months is presented up to the lower mesosphere and compared with previous studies. In the stratosphere some new features of the effective diffusivity distribution are obtained. For example, there is a local maximum of the effective diffusivity at midlatitudes of the Northern Hemisphere of the summer middle stratosphere. The effective diffusivity fields in the lower mesosphere show a strong increase of the mean effective diffusivity from the upper stratosphere to the lower mesosphere and the existence of a complex latitudinal structure of the effective diffusivity at mesospheric heights. In the lower mesosphere there is a marked interannual variability during the Southern Hemisphere easterly wind development. A possible explanation for the obtained structure is discussed on the basis of in situ Rossby wave generation and Rossby-wave-breaking effects.