Surrogate groups have been used as a useful tool for biodiversity conservation. The occurrence and distribution of a taxon can be predicted based on the occurrence of other biological species or groups. Consequently, the current study sought to determine the presence of one or more surrogate groups in a seasonally flooded region in the South American Pantanal wetlands. Data on the occurrence and distribution of species were collected at Pantanal Long-Term Sampling Sites (PLTSS). We assayed for congruence between woody plants, herbaceous plants, spiders, anurans, birds and small mammals using Mantel tests. We also evaluated the effect of selected environmental and spatial factors on each biological group, using variance partitioning. Based on the average correlation between groups, the group with the highest congruence was woody plants, and it was therefore considered the best surrogate group for the PLTSS area. The soil texture (percentage of silt, sand and clay) are not important in defining plant group distributions. However, plants were distributed as a function of flood intensity and hydroperiod. The effect of flooding and vegetation structure differed between the analyzed zoological taxa. Additionally, spatial factors, here represented by Moran Eigenvector Maps, were important for all evaluated biological groups.