The occurrence of sporadic E (ES) under the main F region trough has been established using ionograms from a vertical incidence ionosonde at Halley Bay, Antarctica (76°S, 27°W; L = 4.2), a site well suited for such studies as the trough can be seen under a wide range of magnetic conditions and local times. Analysis shows that ES is very frequently observed under both the equatorward and poleward edges of the trough, as well as poleward of it. Before magnetic midnight, ES layers with semi-thickness similar to those of the normal E layer are most common. This is in marked contrast to the layers seen after magnetic midnight which usually show the characteristics of thin ES layers. Additional information on the morphology and dynamics of ES layers associated with the main trough has been provided by detailed study of individual events using data from the British Antarctic Survey's advanced ionospheric sounder recently deployed at Halley Bay. A possible explanation of the observed change in the ES layer characteristics at about magnetic midnight is related to differences in the type and spectra of the precipitating particles. The effects of transport processes in the E region are also considered as a possible cause. It is shown that the redistribution of ionization by the convection electric field may be important.