Context . The processes of fragmentation, habitat loss, degradation and their combined effects are formidable threats to amphibian populations.

Aims . We evaluate the effect of three land use-type variables and nine landscape matrix quality factors on amphibian presence in four coffee agro-ecosystems and two cloud-forest fragments in central Veracruz, Mexico.

Methods . Each site was thoroughly searched using the visual-encounter survey technique along different trails in the most feasible microhabitats for detecting amphibians during four rainy seasons (2005, 2006, 2008 and 2009). Centred on the location where each amphibian species was first recorded, we established what we refer to as a buffer area within a radius of 1.5 km. A Co-Inertia mathematical model was used to determine which of the explanatory variables contributed to maintaining amphibian diversity. The landscape variables were landscape-quality index, open areas, canopy cover (low, intermediate, dense) at the matrix level, river, road and human population density and site size. Local variables were elevation, plant-structure and biological-impact indices.

Key results . During the study we recorded 1078 amphibians belonging to 26 species, 17 genera and 10 families. The variables explaining the composition of amphibian diversity were river and human population density, low canopy cover at the matrix level, elevation, site size and plant-structure index. Amphibian diversity increased as the structural complexity of the habitat increased, and the former was positively correlated with fragment size.

Conclusion . The present study indicated that coffee agro-ecosystems and the cloud-forest fragments in the region form a gradient in habitat quality and landscape variables that exert a differential influence on amphibian assemblages, and that each species responds uniquely to different variables.

Implications . Coffee agro-ecosystems and forest fragments cannot be seen as homogenous patches with a certain habitat quality, separate from the landscape matrix in which they are immersed. Stakeholders are not advised to rely on a single strategy to conserve the amphibian community, but rather should aim to maintain a heterogeneous landscape with forest fragments and coffee agro-ecosystems that have a complex vertical plant structure at the habitat level, especially in highly river-dense landscapes.