The present club was founded in 1998 following the merger between two separate local clubs, AFC Lymington of the Wessex League and New Milton Town of the Hampshire League and until the end of 2006/07 season was called Lymington & New Milton F.C. with The Linnets as the nickname.

Formed in 1898, New Milton F.C. competed in both the Bournemouth & Hampshire Leagues and changed its name to New Milton Town when the Town Council offered the chance to relocate in 1993 to Fawcetts Fields, helping to complete the best sports facility in the New Forest. This base allowed the club to compete in Wessex League football.

Formed in 1875 Lymington Town F.C. had also enjoyed a long period of involvement at Hampshire League level playing at the town’s Soprts Ground, sharing with Lymington Cricket Club. In 1986 the club became a founder member of the Wessex League and, in 1988, merged with local rivals Wellworthy to become AFC Lymington.

With Tony Veal in the Chair and John Mills as Manager the new club got off to a dream start finishing in 5th place and winning the Wessex League Cup for the first and only time when the red hot favourites, Havant, were beaten 3-1 in the Final.

In 1992/93 with john Mills in the Chair and former Welsh amateur international, Trevor Williams, as Manager the Wessex championship was won for the first time after finishing runners up the previous season. To cap a wonderful season, the reserveside under the management of Derek Binns ran away with the Combination title. The following year saw the club finish 3rd but silverware was gained when the Russell Cotes Cup was won for the first time since the 1930s.

After missing out by a point in 1995/96 the title returned to the Sports Ground in 1996/97 with Derek Binns as Manager and the title was successfully defended the following season. An application to the Southern League failed on ground grading requirements. The proposed solution of a merger with New Milton Town and a move to Fawcetts Field split the club but for season 1998/99, a new club called Lymington & New Milton played in the Wessex League. That season the championship was won again and the club progressed to the last 8 of the Vase losing 3-1 to Taunton Town. Once again ground grading thwarted the club’s ambition of playing in the Southern League.

In 1999/00 the club finished runners up to Wimborne and reached the 4th Qualifying Round of the F.A. Cup losing to Aldershot Town in front of a record 1500 crowd. Derek Binns stepped down the following season and long standing player, Graham Kemp, took the reins. In 2002/03 his first full season the club finished 6th which was replicated the next season despite Kemp stepping down and the loss of key players.
In June 2003 former Totton boss was appointed as Manager with Richard Phippard as his Assistant. The completely rebuilt side finished 4th and again reached the 4th Qualifying Round of the F.A. Cup losing to Salisbury City.

2004/05 started with 3 losses in the first 5 games but then went on a run of only two losses in 37 games to win the title on the last day of the season against Gosport Borough. A strong Cup run ended in a replay at Conference side, Woking, and a loss in the last 16 of the Vase to a last minute extra time goal at Bury Town.

The title win gained promotion to the Isthmian League Division 1 for season 2005/06 finishing 16th. The following season the club was transferred to the Southern League Division 1 South & West. After a bright start financial pressures took their toll and despite finishing 17th, permission was sought to return to the Wessex League.

Trevor Parker initially took over the managerial reins and rebuilt the side completely. The club became stronger as the Wessex Premier season went on. Andy Bye and Paul Masters took over from Trevor in mid season and the club went on to finish 19th but are looking to improve on that position in 2008/09.