In every eukaryotic organism, unidirectional cell cycle progression is driven by controlled proteolysis. Here, we present the identification of two ubiquitin ligase complexes in the diatom Phaeodactylum tricornutum, the SCF and APC/C, being important for temporal controlled degradation of key cell division proteins. We annotated and analyzed the conservation of all subunits of both complexes in P. tricornutum. Expression analysis during a synchronized cell cycle showed that the SCF complex subunits are transcribed at the G1-to-S phase transition. In contrast, expression of the APC/C subunits is relatively constant, except for its activators that are differentially expressed: CDC20 is highly expressed at mitosis, while CDH1 is transcribed at late M and during G1, suggesting temporal activation of the different complexes. Furthermore, we performed in silico prediction of APC/C targets through destruction box (D-box) and KEN box analysis, two known degrons for substrate recognition of the APC/C complexes. For this, we focused on the expanded set of diatom cyclins, including the diatom-specific cyclins. Interestingly, we could find D-boxes for most mitotically expressed cyclins, but also some of the G1/S cyclins. Thus, it appears that in analogy with what is known in other organisms, tight post-translational control of the diatom cyclins might contribute to the well-coordinated cell cycle progression.