A newly discovered 1000-km scale longitudinal variation in ionospheric densities is an unexpected and heretofore unexplained phenomenon. Here we show that ionospheric densities vary with the strength of non-migrating, diurnal atmospheric tides that are, in turn, driven mainly by weather in the tropics. A strong connection between tropospheric and ionospheric conditions is unexpected, as these upward propagating tides are damped far below the peak in ionospheric density. The observations can be explained by consideration of the dynamo interaction of the tides with the lower ionosphere (E-layer) in daytime. The influence of persistent tropical rainstorms is therefore an important new consideration for space weather.