Parasites, bacteria, insects, anything I can't see very well that looks alien and can kill me, hurt me, make me sick etc. Insects all look like miniature monsters to me, with the exception of ladybirds, bumble bees, and mantises - they all freak the hell out of me, I don't know why insects have to look so bloody hideous - and then when you add all those pincers and venoms, I freak out. I hate Spiders as well and while I know they're not insects (I get the "Spiders aren't insects argument" a lot.) I still kind of think of them the same way, why do they have to be so goddamn scary looking? If the hobo spiders that are invading my home looked a little nicer and didn't have necrotic bites, I wouldn't be throwing boulders around my house trying to squish them. In fact I do respect and have a fascination with spiders, as long as they're trapped in a glass and at least 2 rooms away. I actually love the fact that they keep the flies out of my house but I still pansy out when I see one.
When it comes to microscopic things, they also look terrifying (The Metroids scare the shit out of me solely for kinda looking like one. Oh and they're parasitic so egah.) and can often cause bad things to happen to you. I'm not a die-hard germophobe, but I do like being clean and I do get uneasy in really dirty rooms. Parasites are the be all, end all fear of mine though. The thought of something living in or on my body, slowly killing it without my knowledge is just downright horrifying. Anything that leeches or feeds on a living being is the scariest thing I can imagine, especially the ones you won't see without a microscope. The ones you can see freak me out less, but that's not saying much since I literally went psychotic when I saw a tick in my arm.
I'm also afraid of things that live in water. Ocean creatures look fucking weird and alien, and I have nightmares about being in the ocean and seeing these things. I also hate it in video games when they throw in something weird in the water, I always shit my pants even if it is just a clownfish.
I could write a whole book on some of the others, but I am sure this post is already TL;DR.