Place rabbit in a container with lid. Season with a teaspoon of salt and a pinch of pepper.
Cover with onions, bell pepper, thyme. Add the wine. Close with the lid and marinate overnight in the refrigerator.
Remove the rabbit from the container, shaking off the excess liquid. Reserve the marinade.
Heat the oil in a heavy-bottom pot. Add the rabbit and brown (careful with splatters!). Cover with a lid. As the liquid evaporates, stir frequently, adding water by the tablespoon.
Once the meat is cooked through (it should be quite tender), let the liquid evaporate. Brown again. Stir in the peppers, onions and thyme from the marinade. Cook over very low heat until the onion has become translucent. Sprinkle with the flour and stir well, in order for the flour to cook throughout without burning. Add the cooking wine from the marinade and stir vigorously until it has mixed with the flour.
Simmer over low heat until the sauce thickens. Season with salt and pepper to taste.