Honeybees at work on their hive. Pat Greenhouse | The Boston Globe | Getty Images

Home Depot and Lowe's are under fire for selling pesticides that some believe are partly to blame for killing billions of the nation's honeybees. Petitions with thousands of signatures are being delivered to the home-improvement retailers this week, demanding they stop selling the pesticides—called neonicotinoids—along with any plants in the stores that have been treated with them. Neonicotinoids are the most widely used class of pesticides in the world. "There's a growing body of science indicating that the pesticides are a key factor in recent global bee deaths," said Lisa Archer, director of the food and technology program at the environmental group, Friends of the Earth.

Archer said her group, which is leading the petition effort, tested plants for sale at Lowe's and Home Depot and more than half had the pesticides. She said because there were no labels on the plants or pesticides that they could be harmful to bees, consumers were left in the dark about the dangers. (Read more: How the Pacific could be California's drought fix)

Home Depot was aware of the pesticide issue before the petition effort began, said Ron Jarvis, vice president of merchandising and sustainability at the retailer. "We've been in contact for months with several environmental groups about neonicotinoids," Jarivs told CNBC by phone. "Now we've been in contact with Friends of the Earth."