Applying for Phd at two different departments, in the same university, but very relevant fields. Would it harm my admission? Biophysics and Condensed matter physics interests me. I am more inclined towards biophysics. 
Would it weaken my application if i applied to both the biophysics program (Biological sciences department) and the condensed matter program (Physics department) in the same university? I want to apply for Condensed matter, in case i didn't get accepted in biophysics, i might get accepted in condensed matter.

P.S. I have a Bachelor's degree in theoretical physics.
I would see no harm in doing so. I view it as akin to applying to different schools when you first start college. To gain a better understanding, I would contact the graduate office at your school about multiple applications to different departments. Policies do vary from campus to campus.