Would taking bactrim (sulfamethoxazole and trimethoprim) for 2 days make me falsely negative for chlamydia? it was a pcr test.

Probably not: Sulfamethoxazole-trimethoprim (Bactrim) can suppress chlamydia, so it could lead to a false negative test result. However, 2 days is too soon. Even with the most effective antibiotics against chlamydia (e.g., doxycycline, azithromycin) it usually takes a few days for DNA tests (like PCR) to become negative. So your result probably is reliable. But if in doubt, discuss with the doctor or clinic.