Heat the oil in a stockpot over medium. Add the chiles, onion, and garlic; cook, stirring often, until tender, 6 to 8 minutes.
Add the vinegars and red pepper flakes. Bring to a boil; cover, reduce heat to medium-low and simmer until vegetables are tender, about 20 minutes.
Stir in the salt, and remove from the heat. Let stand 20 minutes.
Process the chile mixture in a blender or food processor until smooth, stopping to scrape down the sides. (Remove the center of the blender top to prevent the mixture from overflowing, and be wary of inhaling pepper vapors.)
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