Cephalanthera, Limodorum and Neottia, which are known as primitive orchids, are rhizomatous orchids and commonly distributed in Turkey. This study aims to investigate orchid seed variation between some representatives of Neottieae, Cephalanthera rubra, Limodorum abortivum, Neottia nidus-avis, and Neottia ovata, naturally distributed in Turkey by using geometric morphometric analyses based on 2-dimensional landmarks. For this purpose, a total of 95 specimens were evaluated and photographed using scanning electron microscopy. Using software, 12 homologous landmarks were obtained to reflect the main aspects of the seed shape. Species were compared with various statistical methods by calculating the data obtained from shape and size variables with the Procrustes method. The difference in both size and shape were significant between the species. Shape differences were most prominent in the chalazal and micropylar regions of the seed as well as the whole seed width. Discriminant analysis and cross-validation scores were a highly powerful to distinguish the species with scores ranging from 60% to 88%. Regression analyses also revealed allometric effect of the size on seed shape with a similar trend across species. Based on current results, geometric morphometric analysis is encouraging in the research of structural variation within plant parts. The present study is also significant in terms of the widespread use of such studies in the field of botany, especially in the context of systematic or functional morphology.