Mirroring its South Wales counterpart the Welsh Football League Division One, the 16-team division forms half of the second tier of the Welsh football league system and falls one level below the nationwide Welsh Premier League.
[1] Caernarfon Town were champions in the previous season but were ineligible for promotion to the 2016–17 Welsh Premier League; the promotion spot instead passed to runners-up Cefn Druids.
No teams in the previous season were relegated from the top-flight into the Cymru Alliance; both Haverfordwest County and Port Talbot Town dropped into the 2016–17 Welsh Football League Division One.
Only the bottom-placed team from the 2015–16 Cymru Alliance, Rhayader Town, were relegated to a third-tier district league for 2016–17, the Mid Wales Football League Division One.
Two teams were successful in the 2015–16 Welsh third-tier leagues and were promoted in Rhayader's place: Penrhyncoch and Ruthin Town.