Most well-known bacteria (for example, all known disease-causing organisms) fell into one of the two distinct groups. The other group contained many bacteria which lived under extreme conditions including conditions which may have been present on the early Earth. As a result, the division was the "main" ("true") bacteria, and the "older" bacteria. The nomenclature of this division was inaccurate, but it has stuck.
The distinction is based on subtle features: their ribosomal RNA composition was the original dividing line and since then, it has been shown that there is also a distinct difference in their membrane lipid composition.
