We've been breeding bees for millennia. Maybe 7000 years or so. We're pretty good at it.

Honeybees are domesticated animals, like dairy cows. When we need more, we breed more. There's no threat to domestic honeybees as a species or even as an industry. Unlike the native bees, which are being threatened by introduced diseases (both from non-native introduced species like honeybees, and through bulk imports of honey from other continents), encroachment of non-native species (did you know native bees in North America can't pollinate European or Asian flowers?), and possibly pesticides.

I lose hives every year (from winterkill to bear attacks and my own stupidity). A new nuc ("starter pack") is about $300. It would be cheaper and easier to steal from my neighbours, except I have morals.

There was a link on HN a few months ago discussing a new strain of bees [0] being bred up in Canada that are supposedly much more resistant to some of the mites and diseases that are commonly affecting hives. As far as pesticides go, though, I'd imagine that it's going to be pretty hard to develop an insect that isn't affected by chemicals carefully engineered to affect insects; we're going to have to shift away from using these sorts of treatments, neonicotinoids especially, in our agriculture.

[0] http://www.saskatraz.com/index.htm

Iirc they tried to create a mixed breed with africanized bees which are supposed to be much more hearty. But I think the problem was that they don't mix well the stronger just takes over the weaker.

The honeybee is a domesticated species, and there are breeding programs set on making honeybees more resistant to the mite and virus that are often the cause of colony collapse. It's a tricky process though.

My guess is that genetic engineering of the bees or their microbiome will end up being the solution.

Or we can just let them all become africanized...