Forty-three individual adult weedy seadragons Phyllopteryx taeniolatus were identified from underwater images using patterns of spots and blotches on the lateral surface of the abdomen. These patterns were unique and did not change over the 18 month course of the study and could therefore be used to identify individuals when estimating population variables using non-invasive capture–mark–recapture and accumulation curve methods. Two similar neighbouring sites in southern Tasmania showed considerable differences in their estimated populations of P. taeniolatus. Estimated annual survival was >80% at one site suggesting that P. taeniolatus may be considerably longer lived than other syngnathids with a maximum life span in excess of 10 years. Males incubating embryos were observed from October to March and at least two clutches could be borne during this period. This technique of photo-identification could provide a cheap and effective way to monitor populations of this iconic species across its range, particularly in conjunction with optimized pattern-recognition software.