Infra-specific variation in phenotypes of bryophytes is rarely shown to be spatially or ecologically structured. By using a morphometrics approach based on more than 2,300 measurements of nine gametophyte characters taken from 63 specimens across the global range of Syrrhopodon leprieurii Mont. (Calymperaceae), we demonstrate through partial and total Mantel analyses that phenotypes vary significantly over distance and elevation. Furthermore, S. leprieurii specimens of montane and spatially isolated (island) regions (such as the Andes and Cuba) exhibit disproportionately greater morphological differentiation over relatively shorter distances when compared to those from lowland rainforests of the greater Amazon basin. Structured morphological variation among bryophyte populations is uncommon and we suggest that, in light of results from studies of other Neotropical plant taxa, more pronounced differentiation in niche structure in this region may account for such variability.