An overview of recent searches for new physics with top and bottom quarks in the final state is presented, using proton-proton collision data collected with the CMS detector at the CERN LHC at a center-of-mass energy of 13 TeV. The presented analyses search for partners of standard model particles: an excited bottom quark $b^{*}$, new massive boson $W^{'}$ or top quark partner $t^{*}$. Jet tagging techniques are used to reconstruct and identify jets originating from highly boosted objects in order to improve sensitivity. No significant deviation from standard model predictions are observed, therefore stringent exclusion limits on the production cross sections of all analyzed particles are set. A range of different particle masses and chirality hypotheses are considered.