CuInS2 nanocrystals were synthesized by thermal decomposition of the molecular precursor [(Me3P)3Cu(SC2H4S)IniPr2] in the presence of oleylamine in dioctyl phthalate. According to X-ray diffraction patterns, the as-synthesized CuInS2 nanocrystals crystallize in the wurtzite type structure. High-resolution transmission electron images and selected area electron diffraction patterns reveal a nanodomain structure. The individual domains are approximately 5–10 nm in size and characterized by short-range cation ordering, which assuming hypothetical long-range order, corresponds to an orthorhombic superstructure (space group Pmc21, a = 4.09 ± 0.01 Å, b = 7.16 ± 0.02 Å and c = 6.56 ± 0.03 Å). The domains are separated by twin and antiphase boundaries.