Next generation sequencing technologies and low sequencing cost has led to an increase in the number of organisms being sequenced and annotated. GOLD lists 6013 eukaryotes projects to be currently underway, as of January 2015. There is a need for an automated pipeline that annotates using a wider range of auxiliary biological data and with new and improved algorithms as the number of eukaryotic genome being sequenced increases. California sea lion (Zalophus californianus), a protected marine mammal inhabiting the western coast of North America, is of considerable interest due to its ability to act as a sentinel species for coastal habitats. As apex predators, like humans on land, marine mammals feed at or near the top of the food chain and have relatively long lifespans that allows the expression of chronic diseases, including cancer, abnormalities in growth and development and reproductive failure. They are one of the first pinnipeds to be sequenced and annotated. The Sea lion genome was assembled into scaffolds using Scaffold_builder and the average length of the assembly increased from 2,179 bp to 25,569 bp and the N50 increased from 2,127 bp to 17,504 bp for all the scaffolds. A comprehensive eukaryotic genome annotation pipeline using MAKER was developed to generate sea lion specific HMM models. This involved multiple levels of evidence including ab initio gene predictors (SNAP, AUGUSTUS and GeneMark-ES), EST evidence and homology evidences.19, 882 sea lion specific genes were generated by the MAKER pipeline and visualized using Apollo software. Functional annotations were performed using InterProScan on the MAKER generated genes. This pipeline will help in future eukaryotic genome annotation work and downstream analysis, especially for novel genomes with little or no auxiliary experimental evidence. The CD-ROM, an appendix to the thesis, is available for viewing at the Media Center in the SDSU Library.