In an earlier paper (Green and Hamilton, J. atmos. terr. Phys.40, 1223, 1978), we reported on a preliminary analysis of six months’ magnetic data from the conjugate stations St. Anthony and Halley Bay, which showed indications of a seasonal variation in the phase differences between Pi2 magnetic pulsations recorded simultaneously at the two stations. We tentatively attributed this behaviour to the different seasonal variation of the ionospheres above the two stations. In this present paper we are able to extend our analysis using 21 months magnetic data, and simultaneous ionospheric data from the Halley Bay station. We confirm the seasonal variation, and from further analysis suggest that it results from an asymmetric damping of the Pi2 signals when the ionospheric boundary conditions at the conjugate stations are not the same.