I just recently found out that i have chlamydia but me and my partner have been together for two years.we both didn't cheat ;what could have happened?

A few possibilities: Chlamydia can be carried a long time, especially in women. Two years is very long but possible. False positive results are rare, but also a possibility. Unfortunately, in most cases like this, it turns out that one or the other partner has had sex with someone else, so you'll need to have a forthright (but sensitive) discussion with your partner. He needs treatment despite his negative test.