Abstract This chapter shows that direct habitat loss is recognized as the main cause of species extinction, and how habitat fragmentation is an inherent consequence of habitat loss. This causal relationship has made the analysis of the relative impact of habitat loss and fragmentation on biodiversity more complex, since their effects are quite hard to distinguish. Model-based approaches underscore the necessity of considering the effect of both habitat loss and fragmentation on genetic variation and dynamics of metapopulations, and further experimental designs under controlled conditions should help validate such predictions. The review material that addressed the consequences of habitat fragmentation on biodiversity repeatedly identified the decrease of connectivity among habitat remnants associated with habitat fragmentation as a major driver of extinction.