The ABC formally launched in February this year to 'encourage debate about the potential production of genetically-modified crops in the UK'.
Since its inception it has used Weber Shandwick in a bid to develop the association's brand and handle media relations work.
Lexington - which will begin the bulk of its work from the start of next year - is to replace WS as the ABC's retained agency after a competitive pitch against undisclosed agencies.
A three-year independent trial of GM technologies - the Farm-Scale Evaluations programme - is due to end next summer. The controversial trials - which have taken place at 200 sites - will have a 'very significant influence on the GM debate', according to Smith.
Lexington's remit will be to present the ABC's case to 'regulators, legislators, retailers and consumer groups', among others, said ABC chairman Stephen Smith, who denied the ABC was an organisation engaged in lobbying.
An information drive to inform the public about GM technology will take place when the trial results are unveiled.
In a letter to The Guardian on 8 June, Smith wrote: 'The industry has not communicated as well as it could have in the past'.
Syngenta, Monsanto, Dupont, Dow Agrosciences, BASF and Bayer CropScience joined forces to set up the ABC.