A fully pedigreed population of the GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus) was established in Malaysia during 2001 and 2002. The selection program was focused on the improvement of growth rate to harvest weight and the mate allocation strategy was aimed at avoiding inbreeding and ensuring that most sire families were represented as parents of the next generation. We examined the build up of inbreeding and we estimated the effective population size by different methods (namely, from: the number of selected parents, the variance in family size, the inbreeding coefficient, and the co-ancestry among selected individuals). The rate of inbreeding was 0.0037 per generation and the effective population size calculated from the rate of increase in the co-ancestry was 88. We conclude that the mate allocation strategy has been successful in containing inbreeding and that the effective population size is satisfactory for the sustainability of the selection program. By contrast, the effective population size is below the minimum (e.g. 500) necessary for the retention of evolutionary potential, hence the population would be unlikely to adapt and cope with severe environmental challenges. The results are discussed in relation to the development and maintenance of selection lines in farmed aquatic animals.