Chipmunks

• Chipmunks are small ground squirrels that burrow, making complex networks of holes and underground compartments for their dens. Chipmunks will occasionally feed on the seeds of the Marigold, located at the base of the flower. They will also consume the roots of the Marigold, and may be burrowing underneath the flowers to get at the root clusters. Spread mothballs around the area and place a few in the burrows to ward off the little nibblers.
  
  

Moles

• Moles are small, nearly blind, burrowing rodents. They emit a high-pitched squealing noise that you may have heard in your garden, and they love to burrow underneath gardens and lawns. They have also been known to feed on Marigold roots, but will not come above ground to chew on foliage and flowers. If your roots are eaten, moles may be the cause. Mothballs work to keep them away, as does human hair spread around the openings and stuffed in to the holes.
  
  

Squirrels

• Grey squirrels are not burrowers, but they do like to use soft, easily dug-up ground--such as that found around your Marigolds--to hide their caches of food. The burrows you are seeing may not be burrows at all, but instead small 6- to 8-inch holes with peanuts and other squirrel staples hidden at the bottom. Squirrels will also chew on Marigold flowers and stems at times. There isn't much you can do about squirrels, as they are not particularly dissuaded by the smell of mothballs. Check your local ordinances regarding setting no-kill traps.
  
  

Rabbits

• Rabbits are voracious eaters, and can chew through a patch of Marigolds in an afternoon. Their burrows are much larger than those made by chipmunks or moles, and have rabbit warrens at the bottom, used to hide young in the Spring. Rabbits are not good climbers, so placing fencing around your Marigold garden will likely keep them out, and keep your flowers safe.