There is a pressing need to assess resilience of coastal ecosystems against sea level rise. To develop appropriate response strategies against future climate disturbances, it is important to estimate the magnitude of disturbances that these ecosystems can absorb and to better understand their underlying processes. Hammocks (petenes) coastal ecosystems are highly vulnerable to sea level rise linked to climate change; their vulnerability is mainly due to its close relation with the sea through underground drainage in predominantly karstic soils. Hammocks are biologically important because of their high diversity and restricted distribution. This study proposes a strategy to assess resilience of this coastal ecosystem when high-precision data are scarce. Approaches and methods used to derive ecological resilience maps of hammocks are described and assessed. Resilience models were built by incorporating and weighting appropriate indicators of persistence to assess hammocks resilience against flooding due to climate change at "Los Petenes Biosphere Reserve", in the Yucatán Peninsula, Mexico. According to the analysis, 25% of the study area is highly resilient (hot spots), whereas 51% has low resilience (cold spots). The most significant hot spot clusters of resilience were located in areas distant to the coastal zone, with indirect tidal influence, and consisted mostly of hammocks surrounded by basin mangrove and floodplain forest. This study revealed that multi-criteria analysis and the use of GIS for qualitative, semi-quantitative and statistical spatial analyses constitute a powerful tool to develop ecological resilience maps of coastal ecosystems that are highly vulnerable to sea level rise, even when high-precision data are not available. This method can be applied in other sites to help develop resilience analyses and decision-making processes for management and conservation of coastal areas worldwide.