This study examined whether two ciliates could discriminate between equally-sized bacterial prey in mixture and if so, how selectivity might benefit the ciliate population. Live Klebsiella aerogenes, K. ozaenae and Escherichia coli, expressing different coloured fluorescent proteins, were cultured in such a way as to provide populations containing equally-sized cells (to prevent size-selective grazing taking place) and these prey were fed to each ciliate in 50:50 mixtures. Colpidium striatum selected K. aerogenes over K. ozaenae which itself was selected over E. coli. Tetrahymena pyriformis showed no selectivity between K. aerogenes and E. coli but K. aerogenes was selected over K. ozaenae while E. coli was not. This apparent selection of K. aerogenes over K. ozaenae was sustained in ciliate populations with different feeding histories and when K. aerogenes comprised only 20% of the prey mixture, suggesting possible optimal foraging behaviour. The metabolic benefits for selecting K. aerogenes were identified as possibly being an increase in cell biovolume and yield for C. striatum and T. pyriformis, respectively. The mechanism by which these ciliates selected specific bacterial cells in mixture is currently unknown but the use of live fluorescent bacteria, in prey mixtures, offers an exciting avenue for further investigation of selective feeding by protozoa.