Fatty acid (FA) analysis can provide an effective, non-lethal method of elucidating the trophic ecology of fish. One method utilised in the field is to collect biopsied muscle tissue, but this can be problematic in live sharks due to a thick dermal layer with extensive connective tissue. The aim of this research was to determine whether fin and muscle tissue yield similar FA profiles in three species of tropical euryhaline sharks: Carcharhinus leucas, Glyphis garricki and Glyphis glyphis. Fatty acid profiles were detectable in fin clips as small as 20 mg (~ 5 mm × 6 mm) and muscle biopsies > 10 mg mass. Overall profiles in relative (%) FA composition varied significantly between fin and muscle tissues for C. leucas and G. garricki (global R-values = 0.204 and 0.195, P < 0.01), but not G. glyphis (global R-value = 0.063, P = 0.257). The main FAs that contributed to these differences were largely 18:0 for C. leucas, 20:4 ω6 for G. garricki and 20:5 ω3 for G. glyphis, which reflect the different physiological functions and turnover rates of the two tissues. Notably, no significant differences were detected between tissue types for the major classes of FAs and abundant dietary essential FAs. It was concluded that FA profiles from either fin clips or muscle tissue may be used to examine the trophic ecology of these tropical euryhaline sharks when focusing on dietary essential FAs. Given that some non-essential FAs were different, caution should be applied when comparing FA profiles across different tissue types.