In 2007, a review of all well-preserved specimens (including the then-newly discovered Thermopolis specimen) concluded that two distinct species of Archaeopteryx could be supported: A. lithographica (consisting of at least the London and Solnhofen specimens), and A. siemensii (consisting of at least the Berlin, Munich, and Thermopolis specimens). The two species are distinguished primarily by large flexor tubercles on the foot claws in A. lithographica (the claws of A. siemensii specimens being relatively simple and straight).

After scrutinizing some tell-tale bone tissue, a 2009 study found that Archaeopteryx hatchlings had a much slower growth rate than today's chickens and ducks. Instead, the authors speculated that Archaeopteryx had a similar basal metabolic rate to modern kiwi birds, which can take more than five years to reach maturity.