The most significant synthesis of isoindoles (phthalimides) is the dehydrative condensation of phthalic anhydride at high temperature with primary amines (adenine). Novel isoindole analogues with adenine can be synthesized through condensation of phthalic anhydride or substituted phthalic anhydride and purine (adenine). In this study only one type of isoindole analogues (phthalimides) were synthesized using mono bromo phthalic anhydride with primary amine (adenine). Different Mannich bases of isoindole analogues were synthesized using various types of aliphatic amines with variable yields (60- 80%). These Mannich bases were identified and confirmed by FT-IR, NMR and elemental analysis. The antimicrobial assay of these synthesized analogues was tested against H. pylori, E. coli, P. auroginosa, S. typhi, B. subtilis, B. threogensis, S. aureus, MRSA, A. niger, and were found to be active at Minimum Inhibitory Concentration [MIC] range of 125-1000 µg/ml. The most active compounds in the series was S-3 which has shown antibacterial activity against H. pylori at MIC of 125 µg/ml. This compound was identified as lead compounds and further molecular modification is in progress.