Preheat the oven to 400°F. Line a baking sheet with parchment paper.
In a small bowl, mix together the miso paste, grated ginger, soy sauce, honey, sesame oil, lime juice, salt, and pepper until well combined.
Place the baby snapper on the prepared baking sheet. Gently score the skin of the fish in a few places to allow the marinade to penetrate.
Spread the miso mixture evenly over the fish, making sure to get some inside the cavity as well.
Sprinkle the chopped green onions on top of the fish.
Roast in the preheated oven for 20-25 minutes, or until the fish flakes easily with a fork and is cooked through.
Remove from the oven and let it rest for a few minutes. Garnish with fresh cilantro if desired before serving.