We report the synthesis of a novel isotope engineered 13C–12C heteronuclear nanostructure: single-wall carbon nanotubes made of 13C enriched clusters which are embedded in natural carbon regions. The material is synthesized with a high temperature annealing from 13C enriched benzene and natural C60, which are coencapsulated inside host SWCNTs in an alternating fashion. The Raman 2D line indicates that the 13C isotopes are not distributed uniformly in the inner tubes. A semiempirical method based modeling of the Raman modes under 13C isotope enrichment shows that experimental data is compatible with the presence of 13C rich clusters which are embedded in a natural carbon containing matrix.