In a medium bowl, whisk together the lime juice, orange juice, olive oil, minced garlic, cumin, oregano, salt, black pepper, and crushed red pepper flakes (if using).
Place the chicken thighs in a large resealable bag or shallow dish. Pour the marinade over the chicken and seal the bag or cover the dish. Refrigerate for at least 30 minutes or up to 4 hours.
Preheat your oven to 400°F (200°C).
Remove the chicken from the marinade and place it skin-side up on a baking sheet lined with parchment paper. Discard any leftover marinade.
Roast the chicken for about 35–40 minutes or until the internal temperature reaches 165°F (75°C).
Once cooked, remove the chicken thighs from the oven and let them rest for about 10 minutes before serving.
Top your Cuban Mojo Chicken Thighs with fresh cilantro for an added touch of flavor and presentation.