The BL Lac Markarian 501 exhibited two flaring activities in the very-high-energy (VHE) band in May 2009. The lack of correlation between X-rays and TeV gamma-rays without increasing in other bands suggested that more than one emission zone could be involved. Moreover, fast variability in the flaring state was observed, indicating that the emission zones responsible must have small sizes. We use a lepto-hadronic model with two-zone emission to explain the spectral energy distribution during quiescent and these flaring states. In the proposed scenario, the photopion processes explain the VHE flaring activities successfully, and variability constraints place the activity in a zone located near the jet’s base or named inner blob, while synchrotron self-Compton emission describing the X-ray signature during that flaring state occurs in the zone situated far the central engine or named outer blob.