As most terms related to Mediterranean flora, Greek kédros 'cedar' (borrowed into Latin cedrus) has no IE etymology. There're also the derivatives kédris, kédron 'juniper berry' (actually a modified conifer cone).
On the other hand, Latin citrus, which designates two different kinds of tree, 'thuja' (citrum 'thuja wood') and 'citron'1, is somehow related to the Greek word, possibly through an Etruscan intermediate2.
In my opinion, these are instances of a Wanderwort of Semitic origin: *kˁtr- 'smoke, incense', referring to the aromatic characteristics of these trees, either the wood (cedar, thuja) or the fruit (citron).______________________________
1 Whose Greek names: kítron, kítrion, kítrea, are seemingly loanwords from Latin.
2 A. Ernout & A. Meillet (1959): Dictionnaire étymologique de la langue latine, pp. 123-124.