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C. trachomatis is almost exclusively found in humans. There have been reports that trachomas (chronic infections of the eyes) had been described in ancient Egyptian and Chinese manuscripts (http://www.chlamydiae.com/docs/Chlamydiales/Chlamydialeshistory.asp) It was first identified as the cause of trachomas in the 1940's according to my medical textbook (Harrison's). I would imagine it was not known where the exact origin is.
Its has two relatives C. pneumoniae and C. psittaci. C. pneumoniae is also almost exclusively found in humans and I don't know if they know its origin either. However, C. psittaci is virtually ubiquitous and affects many mammals and birds. It is certainly possible it could have evolved from this (much like they think HIV is evolved from SIV--basically the primate/ape/chimpanzee form of HIV). Either that or it has always been somewhat ubiquitous.
C. trachomatis is an obligate intracellular parasitic bacteria, meaning it can only survive in certain environments (obligate), it grows inside of cells (intracellular), and it is dependent on its host for nutrients and survival (parasitic). The species chlamydia is unique (most notably in its method of reproduction) so it is classified in its own order, meaning it is different enough from all other species of bacteria to warrant this. You may remember this from biology.
Its prevalence varies widely based on geographical location (urban vs. rural, etc.), ages, socio-economic class, etc. Additionally since 70% of cases are asymptomatic, lots and lots of people don't know they have it or even suspect. The medical community is generally insufficiently trained to look for it (too many patients, too little time to talk about it with their patients, etc.). In short, it is difficult to say how many people have it. This I am sure you have probably come across already so I won't go on about it. To answer if it is normal flora, I think the answer is no. Normal flora indicates that everyone has it and that it is naturally found there, which I believe is not the case.
As for whether or not it is infectious (meaning contagious), it is. It's just that it does not necessarily cause symptoms that one can feel right away. Its "infectiousness" (medical term virulence) has nothing to do with mutation (although the bacteria does mutate/evolve according to new research; see http://www.sciencedaily.com/releases/2006/11/061116083238.htm).
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Chlamydia trachomatis - USMLEntertainment
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Orignal From: how is Chlamydia trachomatis, the bacteria causing Chlamydia, first formed in a human body?
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