This is the peer reviewed version of the following article:Collins, C., Hall, M., Bruno, D., Sokolowska, J., Duncan, L., Yuecel, R., McCarthy, U., Fordyce, M. J., Pert, C. C., McIntosh, R. and MacKay, Z. (2017), Generation of Paramoeba perurans clonal cultures using flow cytometry and confirmation of virulence. J Fish Dis, 40: 351–365, which has been published in final form at DOI: 10.1111/jfd.12517. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.