Abstract Two separate tectonic blocks in the southwestern segment of the Kazakhstanian orogen, the Chu–Ili terrane and the Karatau–Naryn terrane (with particular attention to Malyi Karatau), are selected to illustrate their geological history and major biogeographical signatures from the Cambrian to the early Silurian. Mid- to Late Ordovician brachiopod and trilobite faunas of Chu–Ili show increased endemicity of shallow shelf assemblages, whereas distinct links to equatorial (‘east’) peri-Gondwanan are more evident in trilobite assemblages of the outer shelf. In the Late Ordovician, strong biogeographical affinities to equatorial Gondwanan faunas became firmly established and they are also traceable into the Silurian. Early Cambrian faunas of Malyi Karatau show remarkable similarity to those of South China. From the Middle Cambrian this region evolved as an isolated carbonate seamount, but until the Early Ordovician links to South China faunas were still evident. Benthic faunas from both regions show weak links to contemporaneous faunas of Baltica and little in common with Cambrian and Ordovician faunas of the Siberian craton. This suggests their location in low southern latitudes, in relative proximity to East Gondwana, which places some constraints on plate-tectonic reconstructions in relation to the southern cluster of Kazakhstanian terranes, including Karatau–Naryn, North Tien Shan and Chu–Ili.