Graeme Jenkins, who was previously chief operating officer at the firm, has taken up the post with immediate effect.
Marshall had been appointed to the post in March 2017 after a 30-year career that included running the Country Gardens and Wyevale chains. He had replaced previous chief executive John Cleland who had spent nine months in the post.
But speculation emerged in the trade media earlier this year that Marshall was no longer involved in day-to-day operations at the firm.
Jenkins had joined the business as chief financial officer in 2016 following the acquisition of Dobbies by Midlothian Capital Partners and Hattington Capital from Tesco.
Andrew Bracey, chairman of Edinburgh-headquarterd Dobbies, said: “The board is delighted to appoint Graeme as our chief executive, having worked closely with him over the last two years.
“We would also like to take this opportunity to thank Nicholas Marshall for his support and leadership during his time as chief executive. The board wish him well for the future.”
Jenkins said: “Dobbies is a great business with an incredibly talented team, and I am very pleased to be appointed as chief executive. We have had a strong start to 2018 and I am confident that we will be able to grow the business successfully over the coming years.”