Chitosan/DNA blend hydrogel (CDB) and chitosan/pectin blend hydrogel (CPB) were synthesized using an emulsion (oil-in-water) technique for the release of methylene blue (model molecule). Both hydrogels were characterized by swelling assays, Fourier transform infrared (FT-IR) spectroscopy, thermogravimetric analysis (TGA) and scanning electron microscopy (SEM), before and after the methylene blue (MB) loading. Higher swelling degrees were determined for both hydrogels in simulated gastric fluid. FT-IR spectra inferred absorption peak changes and shifts after MB loading. The TGA results confirmed changes in the polymer network degradation. The SEM images indicated low porosities on the hydrogel surfaces, with deformed structure of the CPB. Smoother and more uniform surfaces were noticed on the CDB chain after MB loading. Higher MB adsorption capacities were determined at lower initial hydrogel masses and higher initial dye concentrations. The MB adsorption mechanisms on the hydrogel networks were described by the monolayer and multilayer formation. The MB release from hydrogels was studied in simulated gastric and intestinal fluids, at 25 °C and 37 °C, with each process taking place at roughly 6 h. Higher release rates were determined in simulated gastric fluid at 25 °C. The release kinetics of MB in chitosan/DNA and chitosan/pectin matrices follows a pseudo-second-order kinetic mechanism.