An important requirement of many breeding programmes for aquaculture species is the ability to identify organisms individually or at least by family. While a variety of external and internal tagging methods have been developed that can provide efficient identifications systems, most have specific drawbacks. The present study assessed the efficiency of an internal tagging method that can be applied to family selection programmes in crustacean species. Experiments were conducted to test the efficacy of applying visible implant elastomer (VIE) tags to juvenile giant freshwater prawn (GFP). The first experiment assessed performance of VIE tags in juvenile GFP of different size classes and stability of tags placed in different positions in the abdomen with different numbers of tags implanted. The second experiment applied VIE tags in a long term, large scale, field-based farming experiment. The third experiment tested the reliability of the system. Results showed that juvenile GFP at 2 g were of suitable size for VIE tags with no negative effects evidence on growth and survival. Tag retention rates were above 97.8% in all experiments and tag readability rates were 100% with a correct assignment rate of 95% through to mature animal size of up to 170 g.