Translocations are increasingly implemented to assist conservation of declining native species and decrease their extinction risk. Establishing new populations via translocations helps spread the risk of sporadic events leading to extinction, thereby increasing the overall survival probability of the species. But initiating new populations comes with two main challenges: i) the genetic diversity of translocated populations will be reduced compared to the source, and ii) removal of founder individuals will decrease genetic diversity in source populations, placing them at greater extinction risk. We present an empirical study on the conservation of red-finned blue-eye, Scaturiginichthys vermeilipinnis. Several translocated populations have been established with founders sourced from this remnant population. Several generations after re-introduction, we show that translocated populations harbour reduced genetic diversity compared to the remnant population. This is due to i) failure of the founders to capture all the genetic diversity present in the source population, and ii) a failure to retain the genetic diversity of the founders through unbalanced breeding contributions. We argue, prior to undertaking translocations, the trade-off between extinction risk and retention of genetic diversity needs to be determined to establish the optimal conservation strategy to increase the long-term persistence and evolutionary potential of a species.