Localized and sustained delivery of DNA using biomaterial scaffolds would increase the applicability of gene therapy in cancer treatment and tissue engineering. The most promising approach is the application of hydrogel scaffolds to encapsulate and deliver DNA in the form of nanocomplex to the target sites. In the present work, histidine conjugated trimethylated chitosan (HTMC) was synthesized and nanocomplexes fabricated with pDNA at different N/P ratios. The zeta potential and size of the HTMC/pDNA nanoparticles were determined using dynamic light scattering technique and the results were confirmed by scanning electron microscopy (SEM). The morphology of the nanoparticles was found spherical in shape having core-shell nanostructure. Based on gel retardation assay, polyplex dissociation following incubation with heparin, protection against DNase Ι, cytotoxicity and transfection experiments, HTMC/pDNA at N/P 15 was selected as an optimized formulation and loaded into CTS/PF127 and HA/PF127 hydrogel. The optimized HTMC/pDNA nanocomplex was homogenously distributed in the CTS/PF127 hydrogel. Transfection experiments were carried out on HEK293T cell lines and the results revealed that HTMC/pDNA complexes are stable and active inside the hydrogel, however, the transfection efficacy was decreased after incorporation into the hydrogel.