The Ministry of Tourism used to keep track of registered guides, but received so many complaints from travelers that it no longer keeps any track at all. A private association of guides, organized by Jorge Lache of the Amazon Lodge, now keeps a list of guides who are supposedly reputable—though we have no independent confirmation of this. For more information, see Jorge Lache at his office (Marina 592A, tel. 065/25-1078). In general, guides charge US$20–30 per day and use colectivos and canoes as transport.
The one guide we can recommend is Llyacko Manihuari (tel. 065/22-7647, llyacom [at] hotmail [dot] com) who has worked as an area guide for over 16 years and has been involved in the production of several international documentaries about the Amazon [1]. Llyacko (pronounced Jacko) loves to share his knowledge and has a great appreciation for the local communities.
Links:
[1] http://www.moon.com/destinations/peru/the-amazon