The system of phylogenetic classification works differently than the traditional system.

I. Looking at rank

Phylogenetic classification has two main advantages over the Linnaean system. First, phylogenetic classification tells you something important about the organism: its evolutionary history. Second, phylogenetic classification does not attempt to “rank” organisms. On the other hand, the Linnaean classification “ranks” groups of organisms artificially into kingdoms, phyla, orders, etc. This can be misleading as it seems to suggest, for example, that a cat family is somehow comparable to an orchid family. However, they are not comparable:

• One may have a longer history than the other. The first representatives of the cat family Felidae probably lived about 30 million years ago, while the first orchids may have lived more than 100 million years ago.
• They may have a different level of diversity. There are about 35 cat species and 20,000 orchid species.
• They may have different degrees of biological differentiation. Many orchids belonging to different genera are able to hybridize. But the same is not true of cats — house cats (belonging to the genus Felis) and lions (belonging to the genus Panthera) cannot form hybrids.

There is just no reason to think that any two identically ranked groups are comparable and by suggesting that they are, the Linnaean system is misleading.

II. Looking at names

Biologists deal with phylogenetic classification by de-emphasizing ranks and by reassigning names so that they are only applied to clades. This means that your use of biological names doesn’t have to change very much. In many cases, the Linnaean names are perfectly good in the phylogenetic system. For example, Aves, which is the class of birds in the Linnaean system, is also used as a phylogenetic name, since birds form a clade (right).

Most of the specific names that you are accustomed to using (e.g., Homo sapiens, Drosophila melanogaster) have not changed at all with the rise of phylogenetic classification.

However, there are some names from Linnaean classification that do NOT work in a phylogenetic classification. For example, the reptiles do not form a clade — unless you count birds too.