Until recently, the stem gall nematode Pterotylenchus cecidogenus was only registered in eastern Colombia. However, the disease has recently been observed in central Colombian oil palm plantations that use Desmodium ovalifolium as a cover crop. Soil, root, stem, and leaf samples were collected from D. ovalifolium. Plants showed foliar yellowing, leaf drying, and galls within stem nodes. Nematodes were identified, and the distribution, population density, and relative importance of different genera were determined. We performed morphometric and molecular identification of nematodes associated with gall symptoms. The D2-D3 segment of the large subunit-28S of ribosomal ribonucleic acid (RNA) and internal transcribed spacer (ITS) was sequenced, and phylogenetic analysis was performed. P. cecidogenus mainly occurred in the galls and to a lesser extent in the roots and soil. Nematodes were not found in leaf or inflorescence tissue. Morphological and morphometric data confirm the presence of P. cecidogenus in the stems of D. ovalifolium with gall symptoms. This study is the first to report deoxyribonucleic acid (DNA) sequences of P. cecidogenus. Based on D2-D3 and ITS partial sequences, P. cecidogenus is a sister species of the leaf-galling nematode Ditylenchus phyllobius (Sinm. Orrina phyllobia).