Together, Whole Foods and Chobani have become two of the biggest success stories in the food business in the last decade, but now they are parting ways.

Whole Foods said on Wednesday that as of early next year its stores would no longer stock Chobani, primarily because the explosion of Greek yogurt brands has made it more selective in how it allocates its prized refrigerated shelf space.

Chobani, which was founded in 2005 by Hamdi Ulukaya, a Turkish immigrant, and has grown to more than $1 billion in annual sales, helped propel the Greek yogurt craze. Now, Greek yogurt is made by companies like Dannon and PepsiCo, and retailers are struggling to keep up with the increasing number of brands.

“Show me something new,” said John Mackey, co-chief executive of Whole Foods, as he walked past the gleaming yogurt case in the company’s new store in Brooklyn on Tuesday.