Despite the rapid increase in the number and applications of plankton imaging systems in marine science, processing large numbers of images remains a major challenge due to large variations in image content and quality in different marine environments. We constructed an automatic plankton image recognition and enumeration system using an enhanced Convolutional Neural Network (CNN) and examined the performance of different network structures on automatic plankton image classification. The procedure started with an adaptive thresholding approach to extract Region of Interest (ROIs) from in situ plankton images, followed by a procedure to suppress the background noise and enhance target features for each extracted ROI. The enhanced ROIs were classified into seven categories by a pre-trained classifier which was a combination of a CNN and a Support Vector Machine (SVM). The CNN was selected to improve feature description and the SVM was utilized to improve classification accuracy. A series of comparison experiments were then conducted to test the effectiveness of the pre-trained classifier including the combination of CNN and SVM versus CNN alone, and the performance of different CNN models. Compared to CNN model alone, the combination of CNN and SVM increased classification accuracy and recall rate by 7.13% and 6.41%, respectively. Among the selected CNN models, the ResNet50 performed the best with accuracy and recall at 94.52% and 94.13% respectively. The present study demonstrates that deep learning technique can improve plankton image recognition and that the results can provide useful information on the selection of different CNN models for plankton recognition. The proposed algorithm could be generally applied to images acquired from different imaging systems.