Either one will be fine for your purposes. I guess you could say that there is a reason the D90 is $200 more, but the D5000 is also newer. I would be prepared the bet the ISO performance is slightly better on the D90 but I cant say for sure. For flowers you will most likely want a macro lens, and the choices would be the Nikon 60mm f/2.8 or 105mm f/2.8 for floral work either is fine. The extra reach of the 105mm could be helpful for insects and such. Good news is, both the 60mm and the 105mm can also double as a portrait lens, though you will eventually want something wider if you are working in confined spaces. As a beginner you may want to purchase whatever camera you get with an 18-55 or other kit lens. Its always helpful to have a mid range zoom.