The WADA is over all sports for doping as the world organization.
The UCI is the International cycling organization. If you check out their website, you'll see they do lots of stuff with cycling races, from pro road racers to track to cyclo-cross to para-cycling. A small part of what they do, but what we hear about the most, is to test riders for their Biological Passport system. They can test riders anywhere.
Individual countries have their own anti-doping groups over all sports in that country. Cycling is a small part of what they do. The AFLD of France and Coni of Italy pop up the most in cycling news.
I think the Amaury Sports group that own the Tour de France and a lot of other races had some issues with the UCI a couple of years ago (I hope I have that right), so they opted to have the AFLD to the testing for the Tour, and they actually caught riders.
Last year the AFLD found fault with the way the UCI testers worked, claiming among other things that they discussed in a restaurant where riders could hear who would be tested the next morning, and that they showed favoritism to Team Astana by showing up to test and then sitting and having coffee while they waited for riders. The problem with that is that given 20 or 30 minutes, riders can do things that will make their samples come up negative.
This year the UCI has shut the AFLD out from taking samples at the Tour and some other races in France. As an organization that promotes cycling, it's better for the UCI if there are no positive tests, especially with the big names. News about Ricco and others drive away fans.
The AFLD on the other hand is just out to get cheaters in any sport. They don't care how many people watch the sports, and have no vested interest in the success of cycling events.
Italy is really aggressive right now in legal investigations against doping, not just trying to identify and ban individual riders, but to get to the doctors and suppliers and networks across a number of sports.
The AFLD is a government organization. If you look at the thread Bordry, protocols and law enforcement, you'll see that they're now banding together with law enforcement as part of an investigative process to identify and catch doping rings across the world. While the UCI is trying to limit what the AFLD can do, their reach is growing in an investigative sense because they will now request samples from agencies in other countries. So if they're hot on the trail of something that can help the police investigation, they can call the USADA or the Italian agency and ask them to get a sample of someone in that country. And since they're helping to identify networks, they might tie together samples from a cyclist, a distance runner and a soccer player and use them to help the police track down a doctor. They can also now use information from law enforcement to help them identify riders for targeted testing.
The bottom line for me as a pro cycling fan is that the AFLD is aggressive in trying to identify cheaters. On the other hand, it would be really bad for the UCI if say ten top riders were busted at once. And since the Biological Passport system started, they spent way more time than promised just collecting samples and talking to lawyers, because they're scared to death that they'll ban someone based on the passport and run into legal problems because of it. That's why their small successes have been mostly from positive tests by riders they claim to have targeted.
The bad news is that based on recent news, and from some of the products thought to have been used during the Tour last year, and the problems trying to identify own blood transfusions, it looks like the athletes are still well ahead of the testers again. If the sport does get cleaned up, it won't be the UCI that does it, but police and judges.