Based on comparison of morphotectonic analysis results with the SL index analysis, airborne geophysical measurements and field geological and structural data, possible Miocene to Holocene development of the landscape relief of Novohradské Mts. (southern Moldanubian Zone; Bohemian Massif) with a significant contribution of active faulting is interpreted.We suppose a polyphase reactivation of pre-existing faults under (a) the Miocene-Pliocene stress-field (regional ∼ NNW–SSE extension) as (oblique) normal faults trending ∼ SW–NE to ∼NW–SE were responsible for the subsidence of the Třeboň Basin and Kaplice Furrow and (b) the Pliocene to Holocene stress-field (Shmax = 146°) when horizontal in the ∼NNW–SSE direction with possible activity of the prevailing ∼ NNE-SSW trending faults as a sinistral strike-slips or weak reverse oblique-slip movement. The second set of subvertical ∼ WNW–ESE faults was predominantly reactivated in a dextral strike-slip regime or as gentle reverse oblique-slip faults. These Miocene to Holocene events reflect the coupling between the East-Alpine–Carpathian segment and its northern foreland, mainly due to northward motion of the African and the Arabian lithospheric plates.The core of the Novohradské hory Mts. experienced a significant uplift compared to the neighboring areas of the Kaplice Furrow and the Třeboň Basin. The most significant uplift has been found near Rychnov nad Malší, and on the tectonic border between the Kaplice Furrow and the Bukovský hřbet Ridge. This uplift took place during the late Pliocene and Pleistocene, after the sedimentation of lacustrine sediments in the Kaplice Furrow. Although the combination of GIS, morphotectonic and geophysical analyses with validation by field structural data does not provide the final proof of young tectonic activity, we conclude that there is strong indication of Neogene-Quaternary reactivation of several faults in the Novohradské Hory Mts. Based on similar morphological features, it can be supposed that many areas in the Alpine Foreland and Bohemian Massif underwent similar tectonic evolution during the Miocene to Holocene era.