Pollinia is a cohesive mass of pollen. We aim to evaluate the evolutionary trends of pollen morphology within the genus Dendrobium in the light of molecular phylogeny and to test whether pollen morphology may be considered as predictor of inter- and/or intra-specific phylogenetic relationship. A systematic study of 18 species from North-East India was conducted by means of numerical analysis based on 12 micrmorphometric descriptors and SEM ultra-structure. A phylogenetic tree from ribosomal ITS2 sequences was used as reference. Variations in the shape of pollinia were distinct and consistent with five section of the genus Dendrobium and three clads of the section Dendrobium. Other qualitative/quantitative keys to pollinia showed congruence with molecular phylogeny and supported the correlated evolution of these traits. Concurrently pollen sculpturing also showed large variation in exine morphology providing explicit clues for phylogenetic trend of exine evolution. Thus Dendrobium pollen is a good candidate for inferring the genetic relationship at inter- and intra-specific level rather than deducing the ecological adaptation.