Home to a large number of species and indigenous communities, tropical forests across the world are a “melting point” of biodiversity and culture. Tropical forests provide several ecosystem services and form a treasure house for many pharmaceutically important products that have direct benefits to human well-being. However, increase in the anthropogenic activities in recent years has put tremendous pressure on these forests resulting in species extinctions, habitat loss, and fragmentation at a much large scale. Further, indiscriminate harvesting of forest resources has resulted in many economically important species being rendered rare, endangered, or threatened. In these fragmented and anthropogenically impacted populations, conservation action should consider the possible loss of diversity through drift and other microevolutionary processes. The recent developments in the field of conservation genetics and the rapid accumulation of genome-wide data from non-model organisms have enabled their applications in the conservation of these populations and species. However, to date, genetic methods have primarily focused on selected neutral loci to identify units of immediate conservation importance. Recently, next-generation sequencing (NGS) approaches and other statistical methods have been used to understand adaptive variations in fragmented populations. The ability to characterize detrimental and adaptive variation is expected to have tremendous importance for successful conservation efforts. In this chapter, we examine the impacts of forest fragmentation and habitat loss on species demography, fitness, genetic diversity, and evolutionary processes. In particular, we review the existing state of knowledge and discuss novel methods and approaches that could be employed to conserve genetic resources that would not only ensure the survival of the focal species but also maintain ecosystem integrity and stability.