The counting of colonies to quantitate bacteria is an important process in labs for research, clinical diagnosis, and environmental monitoring e.g. in water. Generally counted manually, progress in technology has automated the process through colony counters that can be purchased but can be costly. While efficient, there remains also a challenge correctly detecting clustered colonies compromising inaccurate counts. Leveraging on the smartphone camera, we developed an app that processes images of colony plates and automatically counts them. To provide more accurate counts, the watershed algorithm with distance transform was incorporated into the segmentation and found to distinguish clustered or partially merged colonies better. This app, the APD Colony Counter app, thus transforms the smartphone into a portable colony counter, making the once laborious and tedious process manual colony counting, more accurate, automated and on-the-go.