Up to now, identification of sea turtle species mainly for tracking the population usually relied on flipper tags or through other physical markers. However, this approach is not practical due to the missing tags over some period. Due to this matter, we propose a photo identification system of the individual sea turtle based on the convolutional neural network (CNN) using a pre-trained AlexNet CNN and error-correcting output codes (ECOC) SVM. Experiments were performed on 300 images obtained from Biodiversity Research Center, Academia Sinica, Taiwan. Using Alexnet and ECOC SVM, the overall accuracy achieved is 62.9%. The results indicate that features obtained from the CNN are capable of identifying photo of sea turtles.