The transition regions in thermal structure viz. Tropopause, stratopause and mesopause play a vital role in the vertical coupling of the Earth’s atmosphere. For the first time, interhemispheric characteristics of the transition regions over two subtropical regions are studied using temperature observations from the SABER onboard TIMED satellite and the ERA Interim reanalysis during year 2002 to 2015. Results show that tropopause height is higher over Reunion Island (21.11S, 55.53E) in the Southern Hemisphere (SH) as compared to Mt. Abu region (24.59°N, 72.70°E) in the Northern Hemisphere (NH). Temporal variation of tropopause temperature reveals a decreasing (* 4 K) trend from year 2002 to 2008 and beyond this, an increasing (* 1.5 K) trend is found in tropopause temperature. These features are reinforcing for Mesopause as compared to tropopause temperature. The SH shows stronger variations in Mesopause temperature (* 7 K) compared to NH during year 2002 to 2008. The occurrence frequency of mesopause and stratopause height shows that the maximum occurrence frequency (* 60%) of mesopause at * 100 km in NH, while frequency is found to be * 55% in the SH. Results show that stratopause (mesopause) is cooler (warmer) in NH as compared SH. Moreover, Lomb Scargle Periodogram and wavelet transform techniques are used to investigate the periodicity of mesopause, stratopause and tropopause temperatures and heights. Investigations revealed prominent annual oscillations in the tropopause and stratopause temperatures in both hemispheres. These findings will be of immense use for the vertical and inter-hemispheric atmospheric coupling studies.