Taxonomy is the classification of living organisms. Developed by Carl Linnaeus in 1735. This original form of taxonomy is called Linnaean taxonomy and was based on physical characteristics of plants and animals and does not take evolutionary relationships or genetics into account. I will explain Linnaean taxonomy below then we can move on to evolutionary taxonomy and cladist taxonomy which is far more interesting and more complex.
This rank-based method of classifying living organisms was originally popularized by (and much later named for) Linnaeus, although it has changed considerably since his time. The greatest innovation of Linnaeus, and still the most important aspect of this system, is the general use of binomial nomenclature, the combination of a genus name and a second term, which together uniquely identify each species of organism within a kingdom. For example, the scientific name for Brown House Snakes is Boedon Capensis. No other species of animal can have this same binomen (the technical term for a binomial in the case of animals). The first name will always be the genus, the binomial is the species name and if there is a subspecies a third name is given to it.
A strength of Linnaean taxonomy is that it can be used to organize the different kinds of living organisms, simply and practically. Every species can be given a unique (and, one hopes, stable) name, as compared with common names that are often neither unique nor consistent from place to place and language to language. This uniqueness and stability are, of course, a result of the acceptance by working systematists (biologists specializing in taxonomy), not merely of the binomial names themselves, but of the rules governing the use of these names, which are laid down in formal nomenclature codes.
Species can be placed in a ranked hierarchy, starting with either domains or kingdoms. Domains are divided into kingdoms. Kingdoms are divided into phyla (singular: phylum) for animals; the term division, used for plants and fungi, is equivalent to the rank of phylum (and the current International Code of Botanical Nomenclature allows the use of either term). Phyla (or divisions) are divided into classes, and they, in turn, into orders, families, genera (singular: genus), and species (singular: species). There are ranks below species: in zoology, subspecies (but see form or morph); in botany, variety (varietas) and form (forma), etc.
Example of Taxonomic Ranking for the Brown House Snake.
Species: Boaedon capensis
Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups.  The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.
Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy (producing orderly lists only), in that it builds evolutionary trees. While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants these are known as phylogenetic trees and can be used to classify entire groups of animals right from their long extinct ancestors right up to modern animals. Below is a basic diagram showing the evolutionary classification of reptiles.
Cladistics is an approach to biological classification in which organisms are categorized based on shared derived characteristics that can be traced to a group’s most recent common ancestor and are not present in more distant ancestors. Therefore, members of a group are assumed to share a common history and are considered to be closely related.
Cladists used morphological data but are relying more and more on molecular data (genetics) leading to the field of molecular taxonomy. An example of a clade could be the potential new species of Berg adders where each species is classified by tracing them to their nearest shared common ancestor. Say there are 4 potential species of Berg Adder they would all share a common ancestor Berg Adder 1″ the rest of the species would have diverged from this ancestral species over time resulting in Berg Adder 2, 3 and 4 becoming separate species. To make things a bit more complex new species could have diverged from Berg Adder 4 say Berg Adder 5 and 6, Berg Adder 5 and 6s closed shared common ancestor would be Berg Adder 4.
These new species of Berg Adder would be given a new scientific name based on the rules of nomenclature. Each new species would retain the genus name in this case but would be given a new species name or a subspecies name depending on the degree of change based on genetic studies.
As in evolutionary taxonomy phylogenic trees or cladograms are created when classifying animals using cladist taxonomy.
Below is a basic diagram illustrating a cladogram showing the relationship between reptiles. Note that mammals diverged from their reptilian ancestors several million years ago and shared a common ancestor at a certain period (see the branch off on the diagram). Birds also shown on the diagram were the last group to diverge from their reptilian ancestors and are sometimes grouped with reptiles as some taxonomists consider birds to be highly evolved reptiles, this theory is somewhat controversial.
Genus names can also change as in the case of the house snakes were the degree of genetic change was great enough to split a larger genus into several smaller genera and species were reassigned to these genera as per their genetic relatedness. The African Cobras will also likely go through a genus change with the genus Naja being split into several new genera. The African adders and vipers are also on the cards for a genus split so several new genera will arise other than the genus bitis. Please note that the Berg Adder example is simply an illustration of how this type of taxonomy works and is not based on any current scientific studies.
So why is taxonomy important
You will have to keep up with scientific name changes if you will be applying for permits for indigenous reptiles. If you put the old scientific name for Brown House snakes on your permit application your permit is technically invalid, the same is true should Nat Con put the old scientific name on your actual permit. So you will need to keep up with the newest names if you want to keep our local snakes. Should a species that occurs both in South Africa and Zambia for example and has the same scientific name you will require a permit, should the Zambian species be given separate species status and a new scientific name you will no longer require a permit. This is the case with the Tanzanian Puff Adder which is considered to be the same species as our local Puff Adder and has the same scientific name and thus requires a permit. Should the Tanzanian Puff Adder be given separate species status and a new scientific name you will no longer require a permit to keep them.
With the captive breeding of reptiles it is frowned upon to interbreed species and subspecies. An example of this is Blood Pythons, at one stage Blood Pythons were considered to be a single species and were all imported and bred together as a single species .Resulting in most Blood Pythons bred locally being hybrids which are not as attractive as the separate species are. Now Blood Pythons have been separated into three different species each with their own scientific name. Thus imported Red Blood Pythons that are pure bred or Borneo Short Tailed and Sumatran Short Tailed Pythons should now not be interbred resulting in much nicer looking snakes. It is important to keep up with scientific name changes and taxonomic reclassification in order to keep captive blood lines pure and to ensure you are breeding the correct species together.