A set of eight thiomorpholide-hydrazone conjugates 6a-g and 7 was prepared in good yield by sequential Willgerodt-Kindler reaction on 4-aminoacetophenone then condensation with the considered aromatic aldehydes. The molecular fragmentation of these conjugates by EIMS was interpreted. Structure elucidation of these derivatives was further studied using 1H NMR, COSY, 13C NMR, Dept135 and HSQC techniques. The preferred conformation of the morpholine ring was assigned as the 4C1 conformation. The COSY spectrum of compound 6c showed abnormal deshielding of the N(CH2)2 over the O(CH2)2 protons which was explained. In vitroantimicrobial screening of these congeners with standard antibiotics disclosed their moderate activity against E. coli, S. aureus and C. albicans.