A series of 4-methylsulfanyl benzylidene/3 hydroxy benzylidene hydrazides (1–20) was synthesized and tested for in vitro antimicrobial activity against S. aureus, B. subtilis, E. coli, C. albicans and A. niger. The results of antimicrobial studies indicated that 3-phenylacrylic acid-(3-hydroxybenzylidene)-hydrazide, 16, was the most effective as it showed both bactericidal and fungicidal properties and other compounds possessed bacteriostatic/ fungistatic activity. The multi-target QSAR model demonstrated that the topological parameter, Balaban topological index (J) is effective in describing the antimicrobial activity of synthesized substituted hydrazides.