Crop wild relatives (CWR) can be used to mitigate the negative effects of climate change on crops, but their genetic diversity conservation has not been properly addressed. We propose a new target unit for conservation (Asso-EcoU) based on the occurrence of phytosociological associations in different environments. This approach involves using ecogeographical information and distribution data of associations to identify an optimized set of locations for in situ genetic diversity conservation. Thirty-nine CWR species, grouped in 15 associations, generated 165 Asso-EcoUs. Using the Sites of Community Importance (SCI) of Natura 2000 in Spain, we performed three analyses: (1) gap analysis, (2) coverage of the network, and (3) complementarity analysis. Analyses were performed with both target conservation units, associations, or Asso-EcoUs. The SCI network includes 100% of the associations and 69% of the Asso-EcoUs. The coverage assessment showed that 8.8% of the network is enough to encompass all the networks' target conservation units. Complementarity analysis showed that seven and 52 SCI areas are needed to contain at least one site of the 15 associations and the 114 Asso-EcoUs, respectively. These results highlight the value of Asso-EcoUs to potentially incorporate the genetic diversity component into conservation plans, while increasing the number of species covered.