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You can, but they will be mooshy when you thaw them. I suggest you either dry them or pickle them, depending on the quantity you have and the intended use in the future.
Whenever I freeze jalapenos (or really any kind of pepper), I usually roast them, but if you wish you can freeze them in their raw state. Peppers defrost fairly quickly. Just slip off the skins and you can use them however you want. Because they tend to lose their crisp texture after freezing, I tend to either cook with frozen peppers or chop them finely and add them to a salsa. Frozen peppers will keep in the freezer for at least 6-9 months.