Morphological and molecular diversity among 11 populations of cereal cyst nematodes from different wheat production areas in Morocco was investigated using light microscopy, species-specific primers, complemented by the ITS-rDNA sequences. Morphometrics of cysts and second-stage juveniles (J2s) were generally within the expected ranges for Heterodera avenae; only the isolate from Aïn Jmaa showed morphometrics conforming to those of H. latipons. When using species-specific primers for H. avenae and H. latipons, the specific bands of 109 bp and 204 bp, respectively, confirmed the morphological identification. In addition, the internal transcribed spacer (ITS) regions were sequenced to study the diversity of the 11 populations. These sequences were compared with those of Heterodera species available in the GenBank database (www.ncbi.nlm.nih.gov) and confirmed again the identity of the species. Ten sequences of the ITS-rDNA were similar (99–100%) to the sequences of H. avenae published in GenBank and three sequences, corresponding with one population, were similar (97–99%) to H. latipons.