Drought, in combination with high temperature and low humidity affects the productivity of Hevea brasiliensis, the natural rubber tree and its expansion to non-traditional regions. The genotypes of H. brasiliensis that perform well in traditional regions often failed in non-traditional regions thus necessitating breeding for stress-tolerant genotypes. This can be accomplished by adopting molecular-assisted selection method. Recent developments in identification of drought-responsive transcripts from H. brasiliensis and the findings on role of small RNAs indicate the possibility of employing them as markers for identification of suitable genotypes. In this study, we attempted to identify drought-responsive miRNAs from Hevea brasiliensis through next-generation sequencing (Illumina HiSeq) method. The results revealed the expression of 33 conserved and 32 novel drought-responsive miRNAs. Further, validation of differentially expressed miRNAs by quantitative expression analysis indicated the association of two novel miRNAs, viz., HbmiRn_63 and HbmiRn_42 and two conserved miRNAs, viz., miR168 and miR160 miRNAs with drought tolerance. These miRNAs can be employed as markers for drought tolerance after validation in a larger set of genotypes. This study opens up the possibility of employing miRNAs as markers for drought tolerance in Hevea.