Two series of  benzimidazole substituted oxazole and thiazole molecular scaffold containing divalent isosteres viz oxygen and sulphur were synthesized by reacting 2-(methyl amino)-[(3’’-phenyl-4’’-oxo-(3’’H)-quinazolin)-2’-mercaptophenyl-benzimidazol-1’-yl]-acetyl chloride with thiourea/urea in absolute ethanol medium. Then their corresponding Schiff bases were formed by reacting it with different aromatic aldehydes. The chemical structure of newly synthesized compounds was characterized by elemental analysis, IR, ¹H-NMR and Mass spectra. The Schiff bases were screened for their antimicrobial activity against four bacterial and two fungal strains. The bacterial strains used were Escherichia coli, Alcaligenes faecalis, Pseudomonas aeruginosa and Klebsiella pneumoniae and fungal strains used were Chaetomium globosum and Curvularia lunata. The synthesized compounds were evaluated for qualitative (zone of inhibition) antimicrobial activity by agar cup plate method at three concentrations (500,1000 and 3000ppm). Compound (7d) and (8e) showed good to excellent activity against all the tested strains while others were moderately active.