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This paper proposes a new fiber Bragg grating central wavelength interrogation system by combining evolutionary algorithm and machine learning techniques integrated with an unsupervised autoencoder (AE) pre-training strategy. The proposed unsupervised AE pre-training convolution neural network (CNN) allows training of the convolutional layers independently from a regression task in order to learn a new data representation and give better generalization. It is also used to improve the system accuracy by four times without extra-labeled data. Moreover, AE is combined with a differential evolutionary (DE) algorithm to automate the human labeling task. The proposed autoencoder pre-training convolution neural network and differential evolutionary (AECNNDE) interrogation system achieve good accuracy and can speed-up the computational time by a maximum of 30 times than DE algorithm.