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A novel series of thiazolo[3,2-a]benzimidazole derivatives containing benzofuran nucleus (5a-l) have been synthesized. The key intermediate, substituted benzimidazolsulfanyl benzofuran ethanone (3a-d) was prepared by refluxing the mixture of substituted 2-acetyl benzofuran and substituted 2-mercaptobenzimidazole in acetic acid. The cyclisation of compounds (3a-d) using polyphosphoric acid furnished the corresponding 6-substituted benzofuran thiazolo[3,2-a]benzimidazoles (4a-d). Further, the cyclized compounds (4a-d) were subjected for Mannich reaction to give corresponding Mannich bases (5a-l). All newly synthesized compounds were screened for antifungal and anthelmintic activity. Amongst the tested compounds, 4b and 4d exhibited potential antifungal activity. From the anthelmintic activity data, it was found that the compounds 3a, 3b and 5i were found to be more effective against the tested earthworm Pheretima posthuma. In correlation to anthelmintic activity, the selected compounds were subjected for molecular docking studies and the compounds 3a and 5i have emerged as active anthelmintic agents with maximum binding affinity (−3.7 and −5.4 kcal/mol).