Documentation of scarring patterns on marine megafauna provides a means of quantifying the risk of anthropogenic threats that occur in the open ocean, such as ship strike. This study investigated the rates and putative sources of scarring of whale sharks Rhincodon typus aggregating at Ningaloo, Western Australia. Identification photos of whale sharks were contributed by tourism operators and research groups over a 6 yr period. Analysis of this database found that 355 (38.8%) of 913 whale sharks individually identified between 2008 and 2013 exhibited some form of scarring. This decreased to 15.9% after the omission of categories of minor scarring (nicks and abrasions). An increase in the number of sharks with lacerations between 2008 and 2013 provides some evidence of increasing boat strikes over this time. However, capture-mark-recapture modelling using the multi-state open robust design found no evidence that major scarring influenced the apparent survival or residency time of whale sharks aggregating at Ningaloo. Although lacerations are a useful indication of the level of threat to whale sharks from boat strike, it cannot necessarily be attributed to boat activity in Ningaloo due to the migratory nature of whale sharks in this aggregation, which commonly venture beyond Australian waters. Close collaboration with whale shark tourism operators proved a vital tool to generate the volume of data required for this assessment, and provides a model for similar studies of other megafauna with an associated tourism industry.