The family Molluginaceae (order Caryophyllales) is considered polyphyletic based on the photosynthetic pathway, C4 evolution, and phylogeny of the family. This inference was made based on photosynthetic, anatomical, and molecular datasets. The generic circumscription of this family has greatly been changed owing to the placement of several of its genera into the Caryophyllaceae, Microteaceae, Lophiocarpaceae, and Limeaceae families. However, the generic relationships are largely unknown. By virtue of high substitution rates within the species and the ability to resolve the phylogenetic position of morphologically very closely related species and species complexes, the matK gene has emerged as one of the potential chloroplast DNA molecular markers in plant molecular phylogenetics and DNA barcoding studies. We herein used molecular phylogenetic analyses of matK gene sequences using maximum parsimony and maximum likelihood analyses to infer the generic relationships among currently recognized genera circumscribed under the family Molluginaceae. The resulting phylogenetic tree confirmed the polyphyly of the family Molluginaceae. The genus Hypertelis was found at the base of the Molluginaceae clade. The genus Glinus was close to Glischrothamnus and Mollugo, Suessenguthiella was close to Coelanthum and Pharnaceum, whereas Polpoda grouped with Adenogramma and Psammotropha. The present study constitutes a robust investigation of the molecular phylogenetic relationships among members of the family Molluginaceae. Future study should combine by combined analyses of morphological characters and multiple nuclear and chloroplast DNA sequences with a more comprehensive taxon sampling of the family Molluginaceae.