Strand-specific transcriptomic data was acquired from different tissues from a California sea lion (Zalophus californianus) to provide evidence for gene prediction when annotating genome assemblies. Tissues were collected post-mortem at The Marine Mammal Center (Sausalito, CA) under Marine Mammal Protection Act (MMPA) permit number 18786. The animal (Ensign CSL-13825) was a juvenile male who was euthanized because of poor response to treatment for leptospirosis and streptococcal pneumonia. The sequencing project was reviewed and approved by the National Institute of Standards and Technology Animal Care and Use Coordinator (ACUC), project MML-AR18-0002.