Atlantis II Deep, a submarine basin of the Red Sea, is noteworthy because of its hydrothermally active brine pools. High-resolution temperature records from Poseidon Cruise during February 2011 revealed small steps thermal staircase in the lower transition zone from ≈2002 to 2008/2009 m depth at stations. Four vertically well-mixed convective layers, lower convective layer (LCL) and upper convective layers (UCL1–3), separated by high-temperature gradients at the interfaces were observed. The temperature of the layers UCL1–3 has dropped between 2008 and 2011. The top of UCL3 extends to about 2008/2009 m at stations and its average thickness has increased from 3.3 ± 0.5 m in 1992 to 7 m in 2011, whereas the thickness of layers UCL1–2 has decreased from 25.2 ± 0.3 m to 19.8 m and from 16.4 ± 0.5 m to 14.7 m, respectively, during this time. The upward buoyancy flux is 0.032 to 0.038 × 10−7 m2 s−3 which gives migration speed of UCL3 layer from 0.1 to 0.12 m year−1. With this speed, the thermal staircase ≈6 m thick will merge with UCL3 in 50 to 60 years increasing the thickness from 7 m to nearly 13 m.