There is both a short and a long answer to this question. First, the short and simple: No evidence exists to support the claim that GMO crops themselves have a negative impact on bee populations.
However, the long answer is that there is evidence that neonictinoid pesticides (which are either sprayed on crops, or applied as seed coatings) are seen as a contributing factor to the decline in bee populations. One must consider, however, that currently approved GE crops are modified to either provide protection from pests (for example, using Bacillus thuringiensis, or Bt) or tolerance to herbicides (for example, “Round-Up Ready”)—neither related to neonictinoid pesticides.
Additionally, it’s also important to note that some recent studies have pointed to the indirect effects of Round-Up Ready crops on bees, demonstrating that the reduction in weeds and adjacent non-crop plants leads to reduced pollinator abundance.
The bottom line is that the major causes of bee declines are a combination of (1) heavy pesticide use in agricultural settings, independent of GMOs, (2) habitat simplification and the absence of floral diversity in and around heavily-agricultural areas, and (3) the most likely contributor, heavy pathogens loads from the many viruses, bacteria, fungi, and microsporidia that infect the domestic honey bee.
For more information, I would refer you to the Xerxes Society website on pollinator conservation.
Bryan Danforth, PhD, Professor, Cornell Department of Entomology. Research focuses on the phylogeny, evolution, population, genetics, and conservation of bees.