Abstract. Annual and seasonal variations in the low-latitude topside ionosphere are investigated using observations made by the Hinotori satellite and the Sheffield University Plasmasphere Ionosphere Model (SUPIM). The observed electron densities at 600 km altitude show a strong annual anomaly at all longitudes. The average electron densities of conjugate latitudes within the latitude range ±25° are higher at the December solstice than at the June solstice by about 100 during daytime and 30 during night-time. Model calculations show that the annual variations in the neutral gas densities play important roles. The model values obtained from calculations with inputs for the neutral densities obtained from MSIS86 reproduce the general behaviour of the observed annual anomaly. However, the differences in the modelled electron densities at the two solstices are only about 30 of that seen in the observed values. The model calculations suggest that while the differences between the solstice values of neutral wind, resulting from the coupling of the neutral gas and plasma, may also make a significant contribution to the daytime annual anomaly, the E×B drift velocity may slightly weaken the annual anomaly during daytime and strengthen the anomaly during the post-sunset period. It is suggested that energy sources, other than those arising from the 6 difference in the solar EUV fluxes at the two solstices due to the change in the Sun-Earth distance, may contribute to the annual anomaly. Observations show strong seasonal variations at the solstices, with the electron density at 600 km altitude being higher in the summer hemisphere than in the winter hemisphere, contrary to the behaviour in NmF2. Model calculations confirm that the seasonal behaviour results from effects caused by transequatorial component of the neutral wind in the direction summer hemisphere to winter hemisphere.