Apomixis is production of seeds by asexual means where the progenies preserve the maternal genotype by escaping segregation and recombination. Tapping of this agronomic trait can lead to potential increase in gross agriculture production. However, this trait is lacking in major crop species. Concurrently, efforts have also been directed towards deciphering the molecular mechanisms governing this trait. In recent years smRNAs have been shown to regulate gene function for diverse biological phenomena. We have investigated the possible roles of small non-coding RNAs in apomixis. smRNA expression profiling was done for genetically similar sexual and apomictic lines of Pennisetum glaucum. The apomictic line had two additional chromosomes introgressed from Pennisetum squamulatum into tetraploid P. glaucum. One of these alien chromosomes is known to contain the apomixis locus (Apospory specific genomic region or ASGR). smRNA libraries were constructed from three distinct stages of female gametophyte differentiation : (i) nucellar, (ii) MMC to functional megaspore and (iii) embryo sac development stages. Sequencing resulted in the generation of 22 million tags per sample on an average, of which nearly 70% were redundant tags. Removal of redundancy led to approximately 6 million unique sequences. Most of these sequences were 23-24nt long (81%) followed by 21nt and 22nt sequences. We were able to detect 143 species of known microRNA (miRBase v15) in all the stages with osa-miR168a as the most dominant species whose homolog mir-ath168 is required for AGO1 homeostasis in Arabidopsis thaliana. Out of the 6 million unique tags, only 20 thousand sequences were with read counts of greater than 10 TPM (Tags per million). We analyzed the expression pattern of these sequences between sexual and apomictic stages of gametogenesis. Though a large population of sequences (16,458) expressed in both types of cultivars, 3162 sequences associated exclusively with the apomictic pistils and a lesser number (860) of sequences expressed exclusively in sexual pistils. Differences in expression patterns of sexual and apomictic lines suggest that smRNA might be playing a role in regulation of apomixis. Further analysis of this data will provide valuable insights into the regulation of apomixis.