The invention relates to a method of isomerising a charge comprising hydrocarbons containing between 5 and 8 carbon atoms per molecule. According to the invention, said charge is separated into at least two fractions: fraction A mostly comprising hydrocarbons containing 5 or 6 carbon atoms and fraction B mostly comprising hydrocarbons containing 7 or 8 carbon atoms. Subsequently, said fractions A and B are treated separately under specific conditions in different isomerisation reaction zones.