Champions Cefn Druids were promoted to the League of Wales and were replaced by Holywell Town.
No teams were relegated from the Cymru Alliance, which had operated with sixteen teams in the previous term. Llangefni Town , winners of the Welsh Alliance, and Corwen Amateurs, Welsh National League (Wrexham Area) champions, joined the league on promotion. But the withdrawal of Mostyn on the eve of the campaign, after finishing bottom in 1998/99, saw the Cymru Alliance function with seventeen clubs.
Glantraeth led the way after completing the first half of their fixtures, from Welsh pool Town and Oswestry Town, although Llandudno, with a game in hand, posed a danger to the leading trio. As the season progressed into the final quarter, just four points encompassed Oswestry Town , Flint Town United, Welshpool Town and Glantraeth, with Llandudno still in the championship race. Eventually it was the Park Hall club who prevailed by three points from Glantraeth, despite a three point deduction, to claim their second Cymru Alliance title in five seasons.
Cemaes Bay came out of the pack to finish in third place, above former League of Wales rivals Welshpool, Porthmadog and Flint Town United. Oswestry Town completed a double, after defeating league rivals Buckley Town in the North East Wales Challenge Cup final, but the Park Hall club were unable to claim a treble when they lost to Welshpool Town in the League Cup final. The Maesydre club won their own doule, by retaining the Central Wales Challenge Cup, overcoming Mid Wales League outfit Penrhyncoch in the final.
Glantraeth completed what was to be their most successful season so far, by adding a North Wales Coast FA Cup final appearance to their runners-up position. Unfortunately, the Bodorgan club were overwhelmed 5-0 by Northern Premier League outfit Colwyn Bay in the coast final. The Cymru Alliance flag reached the Third round of the Welsh Cup in 1998/99, with Llandudno and Rhydymwyn losing to Bangor City and Barry Town respectively, while Llangefni Town succumbed, on Anglesey , to Caerleon.
Oswestry Town were able to take their place in the League of Wales, after missing out five years earlier, and they replaced Caernarfon Town in the top flight. Corwen Amateurs' sojourn in the Cymru Alliance was to be a brief one and they returned to the Welsh National League (Wrexham Area), to be replaced by Halkyn United, Welsh Alliance winners, and Welsh