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Objective A system based on image processing technology and Android platform for auto counting colonies is designed,which overcomes the shortages of complicated structure and poor portability of colony counters.Methods The system contains a hardware photographing device to take pictures for colony samples,a mobile application to operate the system.The system uses image processing techniques of spectral threshold segmentation,median filtering,flood filling,open value operation combined with 8-connected boundary tracking algorithm for automatic counting.Results The system can show the colony pictures,count colonies in a mobile phone automatically,and correct the result manually if needed.The system has the advantages of low cost,simple operation,good portability compared to colony counters.Conclusions The relative errors of automatic counting compared with manual counting are less than 5%,meeting the requirements of colony counting.