Abstract Background Detection of characteristic waves, such as QRS complex, P wave and T wave, is one of the essential tasks in the cardiovascular arrhythmia recognition from Electrocardiogram (ECG). Methods A multiscale morphological derivative (MMD) transform-based singularity detector, is developed for the detection of fiducial points in ECG signal, where these points are related to the characteristic waves such as the QRS complex, P wave and T wave. The MMD detector is constructed by substituting the conventional derivative with a multiscale morphological derivative. Results We demonstrated through experiments that the Q wave, R peak, S wave, the onsets and offsets of the P wave and T wave could be reliably detected in the multiscale space by the MMD detector. Compared with the results obtained via with wavelet transform-based and adaptive thresholding-based techniques, an overall better performance by the MMD method was observed. Conclusion The developed MMD method exhibits good potentials for automated ECG signal analysis and cardiovascular arrhythmia recognition.