In a large bowl, whisk together the orange juice, lime juice, olive oil, minced garlic, cumin, oregano, salt, black pepper, and red pepper flakes (if using) until well combined.
Add the chicken thighs to the marinade, ensuring they are fully coated. Cover the bowl with plastic wrap and refrigerate for at least 2 hours, or overnight for best flavor.
Preheat your grill or oven to 400°F. If using a grill, oil the grates to prevent sticking.
Remove the chicken from the marinade, allowing excess marinade to drip off. Discard the remaining marinade.
Grill the chicken thighs skin-side down for about 6-8 minutes, then flip and cook for another 6-8 minutes, or until the internal temperature reaches 165°F. If baking, place the thighs skin-side up on a baking sheet and bake for 35-40 minutes.
Let the chicken rest for 5 minutes before serving. Garnish with fresh cilantro.