Between 2006 and 2011, the Aboriginal and Torres Strait Islander (Indigenous) population grew by between 20 and 30 per cent (depending on whether one uses counts or estimates). Some of this growth was due to an excess of births over deaths (including births of Indigenous children to non-Indigenous mothers). However, much of the growth was also unexplained by the standard demographic balancing equation. Clearly, a large number of people who were not identified as being Indigenous in 2006 were identified as such in 2011. This was also a time when the ABS was linking 5% of the 2006 Census to records from the 2011 Census in order to create the Australian Census Longitudinal Database (ACLD). In the absence of name and address information, this linking needed to be done using other time invariant characteristics, with Indigenous status a variable considered by and ultimately used in this process. However, this changing identification poses a challenge as the extra information gained from using Indigenous status as a linking variable comes at the cost of losing information on identification change, a key piece of information for population projections and other policy and planning exercises. This paper reflects on the use of Indigenous status in the ACLD, what the linking strategy means for our ability to understand the population, and how future waves of the ACLD might be constructed to better make informed policy decisions.