The conversion processes of alternative feedstocks, e.g. biomass and waste, to different fuels result in the formation of light hydrocarbons such as C5/C6 fractions mainly as side products in boiling range of gasoline in a significant amount. The properties of the C5/C6 fractions need to be improved because of their low octane number (< 60) and poor oxidation stability (high olefin content), benzene content, etc. The most suitable process to increase the octane number of these fractions is the skeletal isomerization of the normal paraffins to branched alkanes. The aim of this work was the isomerization of C5/C6 bioparaffin fractions obtained as side-products from special hydrocracking of waste cooking oil to hydrocarbons in boiling range of JET/Diesel fuels. The C5/C6 mixture was isomerized over Pt/H-Mordenite catalyst in a down-flow tubular reactor in continuous operation mode. During the experiments, the process parameters were varied in different ranges, such as the temperature of 220 – 270 °C, the liquid hourly space velocity of 1.0 – 3.0 h-1, pressure of 30 bar, H2/hydrocarbon molar ratio of 1:1. The approach values of the thermodynamic equilibrium concentrations for individual iso-paraffin components in products obtained at favourable process conditions were > 69 – 92 %. The increase of research octane number of the products compared to the feedstocks was higher with > 26 units. By the separation of n-paraffins and single-branched i-paraffins of the products, the C5/C6 isoparaffin mixture could have a high-octane number (= 92). Parallel to the isomerization, the hydrogenation of benzene and oxygen-containing compounds was complete. Accordingly, the utilization of isomerized light fractions of alternative diesel fuel production from different biomass and waste-sources can contribute to the competitiveness of second generation bio-fuels.