Background: The F-box proteins represent one of the largest families of proteins in eukaryotes. Apart from being a component of the ubiquitin (Ub)/26 S proteasome pathways, their regulatory roles in other cellular and developmental pathways have also been reported. One interesting feature of the genes encoding the proteins of this particular family is their variable selection patterns across different lineages. This resulted in the presence of lineage specific F-box proteins across different species. Findings: In this study, 48 non-redundant F-box proteins in E. siliculosus have been identified by a homology based approach and classified into three classes based on their variable C-terminal domains. A greater number of the F-box proteins have domains similar to the ones identified in other species. On the other hand, when the proteins having unknown or no C-terminal domain (as predicted by InterProScan) were analyzed, it was found that some of them have the polyglutamine repeats. To gain evolutionary insights on the genes encoding the F-box proteins, their selection patterns were analyzed and a strong positive selection was observed which indicated the adaptation potential of the members of this family. Moreover, four lineage specific F-box genes were found in E. siliculosus with no identified homolog in any other species. Conclusions: This study describes a genome wide in silico analysis of the F-box proteins in E. siliculosus which sheds light on their evolutionary patterns. The results presented in this study provide a strong foundation to select candidate sequences for future functional analysis.