In vitro morphogenetic ability of plant cells has been demonstrated in diverse species of angiosperms and gymnosperms but no such report is available in the genus Selaginella till date. We have established an in vitro morphogenic root culture where indole butyric acid (IBA) induced profuse branched and unbranched roots in Selaginella microphylla. We observed inter-convertibility of root apical meristem (RAM) to shoot apical meristem (SAM) in presence of IBA and showed that intact roots are also capable of transformation. Friable callus was obtained from roots on prolonged (~50 weeks) root cultures. By isolating total RNA from each of the developmental stages, we performed cDNA synthesis followed by random amplification, sequencing, and BLAST analysis of differentially expressed transcripts to correlate morphological events with the changes on molecular level. The results revealed sequence matches to genes involved in diverse cellular processes such as transcription, translation, photosynthesis, replication, secondary metabolism, stress response, and plant defense suggesting ancient origins of such proteins and the evolutionary conservation of biological function. © 2013 Springer Science+Business Media Dordrecht.