We report a detailed paleomagnetic study on two Plio‐Pleistocene lava flow sequences from the Djavakheti Highland, Lesser Caucasus. The Korkhi sequence is composed of two volcanic successions of distinct age (1.9 and 3.1 Ma), while the Apnia sequence was emplaced between 3.8 and 3.1 Ma according to available radiometric datings. Normal, reverse and intermediate polarities have been determined from both sequences. Mean directions of the normal and reverse polarity groups for each section do not match the expected field direction, but the possibility of tectonic rotations has been dismissed. A composite analysis of paleomagnetic directions, of virtual geomagnetic pole (VGP) scatter and available paleointensity results from a previous study, allow the interpretation of the observed paleomagnetic results. In the Apnia sequence, both a short recording time unable to average paleosecular variation (PSV) and an anomalous Earth magnetic field (EMF) record are responsible for the observed paleomagnetic directions. According to paleomagnetic results and radiometric ages, this sequence most probably records the reverse to normal polarity transition C2Ar to C2An‐3n. The upper Korkhi subsequence yields an anomalous EMF record, reflecting a transitional time interval. Paleomagnetic results and available absolute ages suggest that this subsequence either records transition C2r‐1r to Olduvai or Olduvai to C1r‐2r. The lower Korkhi subsequence registers a normal polarity interval within the Gauss chron, reflecting a stable stage of the EMF.