In a large bowl, mix ricotta, spinach, Parmesan cheese, eggs, and yolks. Stir in nutmeg, salt, pepper, and flour. Form mixture in to small, flattened balls.
Dredge the formed gnudi in flour to coat, tapping off the excess. Slide formed gnudi into the boiling water. Be careful not to overcrowd the pan; work in batches if necessary. Remove the gnudi using a slotted spoon after they float to the top and have cooked for about 4 minutes.
Arrange gnudi on a platter and lightly drizzle with marinara sauce.