Dewaxing by isomerization is one of the most important processes for base oil production of groups II and III. The core of this process is the isomerization of n-paraffins of the feed. While individual paraffin isomerization using different catalysts is thoroughly investigated in many research studies, the effect of zeolites and process conditions on dewaxing by isomerization of different real hydrocarbon feeds is less well known. In the presented work, ZSM-23 and SAPO-11 zeolite-based catalysts were prepared, characterized using different analytical techniques (X-ray diffraction, scanning electron microscopy, transmission electron microscopy, inductively coupled plasma atomic emission spectroscopy, N-2 -sorption, and NH3-TPD), and tested using dewaxing by isomerization of hydrocracked oil and petroleum wax under conditions close to those used in industry. Differences in quality parameters of dewaxed products obtained using different catalysts were also investigated. It was found that the ZSM-23-based catalyst was more active than the catalyst prepared using SAPO-11. While in dewaxing of hydrocracked oil both investigated catalysts showed similar product yields, in petroleum wax isomerization, a SAPO-11-based catalyst was more selective and showed greater yields of high-VI products. It was also established that using the SAPO-11-based catalyst led to dewaxed products with lower density, viscosity, and saturated hydrocarbon content compared with those obtained on the ZSM-23-based catalyst. Findings of this work can help researchers to develop more effective dewaxing catalysts for different hydrocarbon feeds.