Abstract: Watershed transform is the main tool of mathematical morphology used for image segmentation.This method applied directly to gradient image causes severe over-segmentation.We present an improved watershed transform based on morphological reconstruction and flooding by the analysis of the reasons of over-segmentation produced by watershed and the possible under-segmentation due to watershed-plus-marker.The method proposed here is divided into three steps: ① the alternate sequential filters based on reconstruction are used to reduce some difference inside objects;② the area oriented flooding and depth oriented flooding are applied to gradient image in order to fill some local minima that does not correspond to maximum and minima in original image;③ the processed gradient image is segmented by the watershed transform.The method proposed here can effectively control watershed transform and reduce over-segmentation and under-segmentation.