Here is information I have found :
The Southern Jungle
Manu Biosphere Reserve
No other park in the world can equal Manu for species richness. Over 1000 birds have been identified, 15000 plants and 13 species of monkey as well as millions of insects. In Manu there are healthy populations of jaguar, tapir, black caiman and the giant otter. These animals have not been subjected to widespread hunting as they have in many other jungle areas and are therefore less fearful of humans, increasing the possibility of actually catching a glimpse of them. Access to the Manu Biosphere Reserve is from Cusco, traveling with one of the recognized Manu Agencies.
Tambopata Candamo Reserved Zone
A number of jungle lodges in the Tambopata Candamo Reserved Zone offer an excellent alternative for those travelers who don't have the time or money to visit Manu. This giant reserved zone contains some of the richest rainforest in the world and includes the entire watershed of the Rio Tambopata which is currently at the forefront of tropical rainforest conservation. Access is from Puerto Maldonado ( half an hours' flight from Cusco)
The Northern Jungle
Iquitos is the northern gateway to the Peruvian Amazon basin. Most tour operators offer trips of at least 2 days, a blend of jungle lodge, camping, and jungle trekking. The protected Pacaya - Samiria National Reserve is located 120km by river from Iquitos and is not usually visited by organized tours although some local tourist agencies can help you with making travel arrangements. Notable wildlife found in the Reserve includes the paiche fish which, weighing as much as 300kg and measuring up to 3m long, is the world's largest freshwater fish. Pink dolphin, giant river turtles, the manatee, black caiman, giant otters, black spider monkeys, common wooly monkeys and many species of Amazon birds can also be observed. One of the most popular jungle lodges is the ExploNapo lodge run by Explorama Tours. Close to the lodge is the famous canopy trail, a system of suspended walkways more than 30m from the jungle floor, allowing a unique viewing experience in the tropical jungle.