Background: Zebrafish possess multiple phospholamban isoforms, one of which has a unique luminal domain. Results: Zebrafish and human PLN have comparable effects on SERCA activity, and both can be reversed by phosphorylation. Conclusion: Despite similar function, the zebrafish sequence variations are context-dependent and not synonymous with human phospholamban. Significance: The different forms of phospholamban in zebrafish may provide a novel SERCA regulatory mechanism.