Well preserved assemblages of cryptospores, chitinozoans, acritarchs, leiospheres, tasmanitids, colonies of Gloeocapsomorpha, scolecodonts and eurypterid fragments from 23 core samples of the Moussegouda core hole in the Erdi Basin, northern Chad, and from two samples from well KW-2 in Kufra Basin, South East Libya are investigated. These palynomorphs were recovered from the southernmost North African marine deposits of Late Ordovician and possibly early Silurian age. The palaeoenvironment evolves from late Hirnantian glacio-marine diamictites to silt-dominated sequences suggesting a marginal marine environment of possibly latest Hirnantian to earliest Rhuddanian age (post-elongata-pre-fragilis chitinozoan assemblages). The recovered palynomorph assemblages are compared and correlated with contemporaneous assemblages recorded in other northern Gondwana localities (Mauritania, Morocco Algeria, Libya, Africa, Saudi Arabia, Jordan), and in South Africa, in order to evaluate possible effects of the ice cap melting on palynomorph assemblages and sedimentation. Our goal is also to improve the regional biostratigraphy across the Ordovician-Silurian boundary. The composition of the recovered palynomorph assemblages, with mixed terrestrial and marine microflora, suggests that the topmost Ordovician or earliest Silurian in northern Chad and southeastern Libya, reflects nearshore conditions, with obvious fresh water influences. The lack of black shale or grey shale in the uppermost Ordovician and of "hot shale" in the lower Silurian in these areas, and their replacement by siltstones, are probably related to an isostatic readjustment that rapidly starved the marine sedimentation in the areas previously overlain by a thick ice cover during the climax of the Hirnantian glaciation. Tasmanites tzadiensis Le Hérissé sp. nov. and Euconochitina moussegoudaensis Paris sp. nov., two new palynomorphs of biostratigraphical interest are described and illustrated.•