The company was founded 10 years ago by David McSweeney, Wilkinson and his wife Michelle. McSweeney, 69, said he had long planned to retire but the death of his business partner had prompted the changeover sooner than he expected.
"Graham thought very highly of Wayne so it is a very good fit," he said. "We started this company 10 years ago and it succeeded. That was an enormous achievement because when we entered the market there was a lot of bad feeling about us. I doubt whether we would be able do it these days because the industry has changed so much."
He added: "Michelle was such an integral part of the company - without her perhaps it couldn't have been as successful as it was."
Smith, formerly of Syngenta, said: "I have worked in the flower seed industry since 1986. I hope to expand the company's assortment, deal with more breeders and bring some new products to the market place."
Flower Seeds Direct currently works with around 50 breeders.
OBITUARY: GRAHAM WILKINSON
Flower Seeds Direct partner Graham Wilkinson has died at home at the age of 53.
Wilkinson went straight from school to begin an extensive career in the seed industry, working in sales for Asmer Seeds in Leicestershire.
In 1988 he was transferred to Nickerson Seeds, where he met Michelle, whom he married in 1992. It was at Nickerson that Wilkinson met David McSweeney.
In 2001 the pair were made redundant and together with Michelle they founded Flower Seeds Direct.
Over the past 10 years the company has supplied UK growers with seed from a wide range of breeders, earning consistent sales growth and a good reputation.
Wilkinson, a keen fan of Leicester City Football Club and horse racing, loved the coast near his home.
His funeral was held on 28 May in Alford, Lincolnshire. He is survived by his wife Michelle and children Lee and James.