Aim <p>Aplastic anemia (AA) is a hematological disorder accompanying with hypocellular marrow and heterogenous characteristics of bi or pancytopenia. This study was undertaken to identify the genetic and epigenetic heterogeneity in telomere maintenance pathway in AA.</p> Materials and methods <p>Peripheral blood samples were collected from idiopathic AA cases (<i>n</i> = 60) and age-matched healthy subjects (<i>n</i> = 43). To evaluate genetic factors, whole exome and targeted resequencing was performed among AA cases and age-matched healthy subjects. Differential gene expression of telomere maintenance pathway and evaluation of predicted miRNA, <i>hsa-miR-1202</i> was assessed through SYBR green based quantitative real-time PCR. The results were then correlated with clinical parameters.</p> Results <p>Majority (95%) of AA cases exhibited significantly reduced average telomere length (p value &lt; 0.001) compared to age-matched healthy subjects except 5% of AA cases. 25 genetic variations in 15 genes were observed exclusively among AA cases with shorter telomere, that may be associated with pathogenesis of Aplastic anemia. Specifically, a heterozygous deleterious variation in <i>TMEM173</i> gene (NM_198282: exon7: c. G878A: p. R293Q, <i>rs7380824</i>) was found exclusively among cases with short telomere that might be used as a possible marker to identify the pathogenic scenarios of bone marrow. Positive correlation of upregulated <i>hsa-miR-1202</i> was found to be associated with their target genes (<i>RAPGEF5</i> and <i>MANEA</i>). Additionally, these altered genes and the <i>miR1202</i> also have a significant negative correlation with platelet count.</p> Conclusion <p>Estimation of average telomere length, genetic variation and gene expression pattern might indicate a novel diagnostic approach towards new treatment regimen of idiopathic AA cases with an emphasis on telomere maintenance pathway.</p>