MicroRNAs (miRNAs) are small RNAs of 22-24 nt in size, known to play regulatory roles by cleavage of target mRNAs or by translational repression. These tiny RNA molecules play important roles in plant development as well as biotic and abiotic stresses. In a changing climate scenario, heat stress is becoming one of the serious threats for food crops production worldwide. Identification of heat stress-regulated miRNAs is crucial for understanding how plants respond and adapt to high temperature stress. In this study, Illumina deep sequencing was performed to sequence sixteen small RNA libraries that were constructed from the shoot and root tissues of 14 days old rice seedlings of heat tolerant and susceptible genotypes. The samples were harvested from seedlings grown under control, short duration stress (SDS), and long duration stress (LDS) treatments. Further, small RNA sequencing was done from seedlings which were given a recovery temperature after a long duration stress. We could map a minimum of 39 known miRNAs in root tissue of heat susceptible genotype treated with LDS and a maximum of 173 miRNAs in shoot tissue of heat tolerant genotype grown under control conditions. In general, number of miRNAs mapped in shoot tissue were greater than root tissue. In addition to known and characterized miRNAs, several uncharacterized and novel miRNAs were also predicted in these samples. Differentially expressed miRNAs were identified from 36 possible combinations of the genotypes, tissues and treatments. The study helped us to understand the differential regulation of miRNAs in root and shoot of heat susceptible and tolerant genotypes of rice. Interestingly, miRNAs regulating recovery phenotype could also be identified. Target gene prediction analysis of these miRNAs suggested many important proteins and transcription factors associated with stress response of plants indicating that the expression dynamics of these miRNAs might play key roles in regulating heat stress response in rice