Assuming humans are the product solely unguided evolutionary pressures, it’s very unexpected that we would have reliable moral faculties. By this I mean our moral faculties (being comprised of both moral intuitions and reasoning skills) would likely lead us to hold largely false beliefs. Of course if God was involved in the origin of man (either by special creation or theistic evolution), it wouldn’t be at all unexpected that our moral faculties were reliable. Therefore the fact that humans have moral knowledge supports theism over evolutionary naturalism.
Why does evolutionary naturalism threaten moral knowledge? Because evolutionary pressures have no way to select between reliable and unreliable moral faculties. Consider for contrast another trait, like a leg. Evolution works on the leg, over generations it will become more suited for escaping predators and moving towards food. The animals that aren’t as well equipped will not get the same opportunities to mate and pass their genes down to future generations. Similarly we can see that having largely unreliable intuitions about the natural world would also deter an animal’s survival. But having true moral beliefs doesn't seem to aid an animal’s survival in the same way having true beliefs about the natural world does. And so it seems an evolutionary explanation of our moral faculties is actually explaining away our ability to have moral knowledge.
Some might object, pointing to evolutionary psychology and its ability to explain why humans would value, for example, altruism. True, a species that works together towards the common interest will be more likely to survive than a species in which each member looks out for only himself. And so we can talk about the survival of not just animals, but of communities of animals and how certain values would promote that communities survival. But this misses the point; such explanations work without taking into account the truth of those value judgments. It doesn’t matter, in other words, that altruism is actually good. All that matters is that exhibiting altruistic behavior increases fitness. But it’s still the case that, given evolutionary naturalism, we’re in no position to trust our intuitions and thus can’t justify this belief that altruism is a good thing.
There are two foreseeable objections to this argument, one that would appeal to a non-natural intuitionist (that is to say, moral properties are non-natural and known through intuition) and the other that would appeal to a naturalist empiricist (that is to say, moral properties are natural and known through observation). The first is maybe the simplest. A non-naturalist could simply reject the evolutionary explanation of our moral faculties. To be clear, he would not be rejecting evolution all together. He may (and indeed still should) believe that the bulk of the human design is due to naturalistic evolutionary pressures, and yet that there are a few traits (his moral faculties being one) that were not produced by evolution. This is a move the theist would himself want to make; that for the most part humans evolved naturally, but then somewhere along the way God tweaked the design and incorporated a few traits that could not be evolved. Now the atheist doesn't have to say God is responsible, in fact he doesn't need to have an explanation at all. The atheist may simply step back and accept this as an unsolved mystery. The theist might think this is silly. After all, why accept a mystery when you can adopt the theistic explanation (and thus theism along with it)? Isn't it rather desperate to reject the theistic explanation in an absence of any alternative? Well it would be, if the theistic explanation was any good to begin with. Typically god-of-the-gaps explanations are not something to aspire to. Though however theism fairs as an explanatory hypothesis in general is debatable, I think we can show that at least in this case it’s a very poor one.
Notice that theism doesn't simply push us onto neutral grounds, but actually raises expectations. If God existed we wouldn't simply find moral knowledge unsurprising, but would expect our faculties to actually be reliable. God after all wants us to be good people; but how can we do that if our ability to discern right from wrong isn't up to the task? It's a simple matter, then, of showing exactly how bad humans generally are at ethical reasoning, and suddenly the argument is turned against theism. Unfortunately humans in general do seem to be rather bad at ethical reasoning. There genuine moral dilemmas that make real life decision making difficult even when we want to do the right thing. Moreover our moral intuitions often lead us to contradictions, forcing us to build theories that preserve the bulk of our intuitions while discarding the fringe cases. Of course this only results in many different (and yet not obviously unequal) ethical theories, making it such a controversial topic. Ethics is, after all, something you study in a philosophy class, and are taught by very educated professors who themselves had to study ethics for many years. Clearly ethics doesn't come natural to humans, at least not to the degree you'd expect if our moral faculties were finely tuned by God.
Already the argument is not fairing well, but there's still more to say. I've explained how a someone leaning towards moral non-naturalism can answer the argument, but now it's time for naturalism's defense. If it turned out that, for example, facts about good and evil reduced to facts about pleasure and pain respectively (or something of that sort), then the problem is solved. Obviously the evolutionary explanation doesn't threaten knowledge of pain and pleasure, in fact if anything evolution predicts it. Pain and pleasure have biological utility, they give evolution a way to praise and punish behavior. The animal who feels pain upon receiving bodily harm will tend away from similarly harmful experiences in the future. And an animal who feels pleasure from sex will be driven to procreate (and thus pass down his traits to the next generation) more often because of it. What this means is that a species which is capable of feeling pain and pleasure will tend to survive better than a species which is not. And so as long as this metaphysical reduction or one much like it holds, we can expect to have reliable moral faculties even if they were solely the product of unguided evolutionary pressures.
The theist may question this reduction of facts about moral value to facts about subjective experience, but then he is questioning a metaphysical belief and not an ethical one. This pushes the heat off our moral intuitions in particular. This is significant because it's not so easily argued that evolutionary naturalism largely undermines our metaphysical intuitions. The theist could grant that evolutionary naturalism doesn't largely undermine metaphysical intuitions in general, but that intuitions about metaphysical reductions seem to be in just as much danger as ethical intuitions. Yes this seems right, but we don't draw metaphysical reductions on sheer intuition anyway. We would give other arguments for the reduction of good and evil to pleasure and pain: whenever one occurs we have the other, it's the best explanation of moral ontology (or, at least, on par with all other decent explanations), and so on. Even if the atheist doesn't want to commit to a reductionistic theory of ethics, we can weaken the ontological dependence and make it much more plausible: maybe moral values simply supervene on or are multiply realized by, among other things, pain and pleasure. This would mean our knowledge of morality isn't perfect—that there's more to the picture than what we can see—but then again we already knew that.