Carboniferous to Permian volcanoclastic rocks have been collected from South Junggar and West Junggar. Primary magnetizations have been observed from the characteristic components of 10 sites of Early Permian (P1) and Late Pemian (P2) red beds of South Junggar area. The 14 Early Carboniferous sites from West Junggar Mountains expose post-folding secondary magnetizations and according to their spatial distribution, 9 remagnetized sites are related to Late Carboniferous - Early Permian granite emplacement whereas 5 sites are located at the vicinity of Late Permian mafic dykes. Two new paleomagnetic poles have been consequently calculated for the periods of P1 at 79.5°N, 36.6°E and of P2 at 60.4°N, 4.7°E, with A95 of 6.8° and 5.4°, respectively. They yield two paleomagnetic poles at 65.3°N, 329.7°E with A95 of 6.3 and 64.8°N, 179.5°E with A95 of 6.9° respectively. Compilation of available data shows stationary and consistent poles for South Junggar area during the Carboniferous and Permian whereas NW Junggar underwent a significant anticlockwise rotation between the Late Carboniferous-Early Permian and the Late Permian, indicating that Junggar was not a rigid block up to the end of the Paleozoic. West Junggar and South Junggar may have experienced contrasting tectonic evolutions. Comparisons of Late Paleozoic poles of Central Asia blocks show: (1) counter clockwise rotation of West Junggar with respect to Siberia, contrasting with the clockwise rotation of North Kazakhstan with respect to Siberia, (2) no significant movements between West Junggar, North Kazakhstan and Siberia since Late Permian, indicating that they were rigidly welded since that time, and (3) anticlockwise rotations of Tarim, Yili and South Junggar with respect to the welded Siberia-Kazakhstan-West Junggar block. Such rotations may have been accommodated by Late Permian to Early Triassic strike-slip faults with an estimation of the displacements of 1570 ± 280 km along the Irtysh-Gornotsaev Shear Zone, 410 ± 380 km along the Nikolaiev-Nalati Tectonic Line and 490 ± 250 km along the Chingiz-Alakol-North Tian Shan Fault since Late Permian time.