It's a fly BUT, in fact, it doesn't actually go into his mouth.
Apparently, according to Paul Freeman who played Belloq a few frames were cut out of the movie where the fly actually flew away.
Q: Can you tell us something about that, and working with the most famous fly in the world?
PF: Ah, yes. I don’t think anybody noticed it during the shoot, there wasn’t any hilarity at that point in the film, and I think if you look at it carefully, if you freeze the frame around that point, you’ll see that actually some frames are missing.
Q: Yeah, I think I noticed that, just a little too jerky.
PF: Yeah, I think they just took out a couple of frames when the fly flew off, just to make the joke. I got a very nice review from Pauline Kayland who noted what a devoted actor I was to go through it, with eating the fly and all.
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