Late Devonian–Early Carboniferous spores recovered from the depths of 2140 m to 2031.3 m in the CSDP-2 Borehole in the southern Yellow Sea are systematically documented to characterize palynological associations for the stratigraphic correlation. The taxonomic study identifies 96 species belonging to 48 genera, including a re-examination of 33 previously described and indeterminate species. Three palynological associations are established for the Wutong Formation in the CSDP-2 Borehole. In ascending order, these are the late Famennian Aneurospora asthenolabrata–Geminospora lemurata (AL) Association from the proposed Guanshan Member, the latest Famennian Cymbosporites circinatus–Asperispora acuta (CA) Association from the lower part of the proposed Leigutai Member, and the Tournaisian Auroraspora macra–Lophozonotriletes involutus (MI) Association of the upper part of the latter member. The AL and CA associations are correlated with the palynological assemblages in the Guanshan Member, and those in the lower to middle parts of the Leigutai Member of the Wutong Formation that outcrops in the suburbs of Nanjing and southern Jiangsu. The MI Association is similar to those derived from the uppermost beds of the subsurface Wutong Formation and is dated as early Tournaisian.