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We have to rely on physical traits instead of DNA in the case of FOSSILS.  Fossils almost never contain DNA, since Fossils are organisms that have been dead for so many many years, so it is not possible to take any samples.

Answer: We rely on the physical traits instead of the DNA when there is no pressence of DNA to be observed.

In case of prokaryotes where there is no true nucleus we need to rely on the physical traits. In case of fossil, no soft tissue is left only hard tissues is left to be studied, in this

There are some more conditions in which there is no pressence of DNA or there is no proper equipment to study DNA.

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