The integration of the "like-minded" research bodies' resources - both bodies are governed and owned by boards of trustees drawn from the horticulture industry - will "give funders confidence to invest in a stable expertise resource", a joint statement from EMR chairman Oliver Doubleday and STC chairman Graham Ward said this week.
The move will also mean the research bodies can boost staff expertise.
Horticultural Development Company (HDC) chairman Neil Bragg said the agreement has been met with "considerable approval" from the HDC board.
It was also welcomed by Sarah Pettitt, chairman of the NFU Board for Horticulture & Potatoes, who said the industry "needs a focus like this to persuade government to commit funding to help us cope with damaging legislation".
HTA director general David Gwyther said the deal "gives real hope that an R&D base for UK growers can now be sustained despite the substantial cutbacks in government funding of research and the devastating effects these are having on providers".
He added: "Maintaining this R&D base is essential if our industry is to survive. This requires high-quality technical innovation in order to both compete globally and to deal with new legislation."
Two key reports published in the past 12 months have highlighted the critical role of R&D in horticulture's success and the damage that has been caused by a fall-off in public funding.
The Commercial Farmers Group last summer warned of a significant decline in the rate of growth of UK agricultural productivity coinciding with reduction in public funding for agricultural R&D.
Meanwhile, the National Horticultural Forum's review of the provision of UK horticultural R&D argued that a successful, innovative horticulture industry could help to deliver some of the Government's public policy aims including those regarding climate change, public health and food security.
Ward told HW he would like to see talks between the industry and the Government on research funding resumed. "When I was chairman of the NFU horticulture board we held talks about this and we were told to wait until the levy boards were brought together. Now it should be back on the agenda."
He added: "The HDC levy should be matched pound for pound. We can fund innovation - but most of what we are having to do is deal with legislation like the imposition of the new EU pesticides legislation. This we cannot do."