Mycoplasma genitalium is not chlamydia. They are two distinct sexually transmitted infections caused by different bacteria. The confusion is understandable: both can infect the same areas of the body, both produce nearly identical symptoms (or no symptoms at all), and both cause inflammation of the urethra and cervix. But they require different tests to diagnose and different antibiotics to treat.
Why People Confuse the Two
Mycoplasma genitalium (often shortened to Mgen) and chlamydia overlap so much in how they present that distinguishing them based on symptoms alone is essentially impossible. In men, both infections cause urethritis, the inflammation of the urethra that leads to burning during urination and sometimes discharge. A study of men attending STD clinics found that both chlamydia and Mgen were independently and significantly associated with urethritis, producing the same core set of symptoms: discharge, painful urination, and itching.
In women, the overlap is just as significant. Both infections can cause cervicitis (inflammation of the cervix), abnormal vaginal discharge, and pain during sex. Both can also be completely silent. Many people with either infection have no symptoms at all, which is part of why both spread so easily.
Key Biological Differences
Chlamydia is caused by the bacterium Chlamydia trachomatis. Mgen is caused by Mycoplasma genitalium, a much smaller bacterium that lacks a cell wall. That missing cell wall matters because it makes Mgen naturally resistant to certain antibiotics that work by attacking cell walls, including some commonly prescribed for other STIs.
Chlamydia is one of the most commonly reported STIs in the world and has been studied extensively for decades. Mgen was only identified in 1981 and has received far less public health attention. It wasn’t until recently that FDA-cleared diagnostic tests became available, meaning many infections went undetected for years.
A Standard Chlamydia Test Won’t Find Mgen
This is one of the most important practical differences. If you get tested for chlamydia and the result comes back negative, that tells you nothing about whether you have Mgen. Standard STI panels typically screen for chlamydia and gonorrhea but do not include Mgen. Diagnosing Mgen requires a specific nucleic acid amplification test (NAAT) designed for that bacterium. There are no point-of-care tests for Mgen, and not all clinics have access to Mgen testing.
Unlike chlamydia, routine screening for Mgen is not currently recommended. There’s no recommendation to screen women under 25, pregnant women, or people on HIV pre-exposure prophylaxis for Mgen the way there is for chlamydia and gonorrhea. Testing is generally reserved for people who have persistent or recurring symptoms of urethritis or cervicitis after other common STIs have been ruled out.
Treatment Is More Complicated for Mgen
Chlamydia is one of the more straightforward STIs to treat. A standard course of antibiotics clears the infection in the vast majority of cases, and antibiotic resistance in chlamydia remains relatively rare.
Mgen is a different story. Antibiotic resistance is a growing and serious problem. A CDC-published study of Mgen samples from France found that 53% carried mutations making them resistant to macrolide antibiotics (the class that includes azithromycin), and 25% showed resistance to fluoroquinolone antibiotics as well. That means over half of Mgen infections won’t respond to what was once the go-to treatment.
Because of this, the CDC now recommends a two-stage treatment approach. The first stage is a week-long course of one antibiotic to reduce the bacterial load. What comes next depends on whether resistance testing is available. If the strain is sensitive to macrolide antibiotics, a high-dose course of azithromycin follows. If the strain is resistant, or if resistance testing isn’t available, a different antibiotic (moxifloxacin) is used for a second week. When resistance-guided therapy is possible, cure rates exceed 90%. Without it, treatment becomes more of a guessing game, and the chance of failure rises.
Long-Term Risks Overlap but Aren’t Identical
Both infections can lead to pelvic inflammatory disease (PID) in women if left untreated. PID can cause scar tissue in the fallopian tubes, ectopic pregnancy, chronic pelvic pain, and infertility. According to the CDC, Mgen during pregnancy may also be associated with preterm delivery or pregnancy loss.
For men, untreated chlamydia can lead to epididymitis, a painful inflammation of the tube behind the testicle, and in rare cases, fertility problems. Whether Mgen causes similar long-term complications in men is still unclear. The CDC states that we don’t yet know if men develop lasting health problems from Mgen.
What This Means If You’re Getting Tested
If you have symptoms like burning urination, unusual discharge, or pelvic pain and your chlamydia and gonorrhea tests come back negative, Mgen is worth asking about. Many people cycle through multiple rounds of antibiotics for “unexplained” urethritis or cervicitis before Mgen is even considered, partly because testing hasn’t been widely available until recently.
If you’re diagnosed with Mgen, your sexual partners need to be evaluated and treated as well. The CDC recommends testing partners and using the same resistance-guided treatment approach when possible. A test of cure, typically 21 days after finishing treatment, is important to confirm the infection has actually cleared, especially given how common antibiotic resistance has become.
The bottom line: chlamydia and Mgen feel the same, look the same on a symptom checklist, and affect the same parts of the body. But they are caused by different organisms, require different tests, and respond to different treatments. If one has been ruled out and your symptoms persist, it’s reasonable to ask your provider about testing for the other.