Modern drug designing incorporates smart use of computer-aided techniques like QSAR, Molecular docking, pharmacophore modelling, etc. In the present work, pharmacophore modelling has been accomplished for acylaminobenzothiazole series as inhibitors of Trypanosoma cruzi. The selected dataset consists of acylaminobenzothiazole derivatives having variety of substituents. The structures were drawn, optimized (MMFF94), aligned and later used to generate a robust consensus pharmacophore model. The results indicate that aromatic rings, H-bond donor/acceptor and lipophilic moieties govern the anti-Chagas activity of selected acylaminobenzothiazole derivatives. The results could be used for future optimization of acylaminobenzothiazole derivatives as Trypanosoma cruzi inhibitors.