Paleozoic evolution of the western Tien Shan, which is built up on the basement of the Karakum continent, is poorly constrained compared to the better investigated Tien Shan terranes along the margin of the Tarim Craton. We present magmatic, metamorphic and detrital zircon ages for the regionally metamorphosed Baisun block and the metasediments comprising the Karakum basement in the westernmost parts of the South Tien Shan terrane. Age spectra of detrital zircon from metasediments of the Baisun metamorphic block and the western South Tien Shan show remarkable similarities over the vast area extending for ca. 500 km and are characterized by major Neoproterozoic peak at 1200–600 Ma and smaller peaks at 2300–1700 and 2700–2400 Ma. The 570–540 Ma ages of the youngest grains define late Neoproterozoic (Ediacaran) – early Cambrian maximum depositional ages of the metasediments. Comparison of the obtained age spectra with those published for the adjacent Tien Shan terranes indicate that the detrital zircon grains in the studied Ediacaran sediments were derived from the southern Precambrian continents of Karakum and Tarim while transport from the Northern Tien Shan was limited. The age of the Barrovian metamorphism in the Baisun block is constrained by ages of anatectic granites in the range 352–340 Ma, corresponding to early Carboniferous. These ages well match the 340–330 Ma ages, established for the adjacent Lolabulak and Garm metamorphic blocks. Based on the regional distribution of suture zones we suggest that during the Carboniferous the relatively small tectonic blocks of the South Gissar comprised an archipelago, located between the larger continents of Karakum and Tarim and possibly connected with the Paleotethys Ocean. The archipelago scenario can explain hot and rapid metamorphic and tectonic processes, documented in the South Gissar, similar to the ongoing collision along the Australia – SE Asia junction.