Tropical pines dominate the plantation forests of South America and Africa. These species have a wide range of uses, from timber production to non-timber forest products. However, since the early 1950s, academia and industry have mostly focused on the genetics of timber yield traits. Therefore, expanding the research in tropical pines to the fields of population genetics and natural adaptive variation would be relevant for innovative uses in conservation and forest tree improvement. In this chapter, we discuss the population genetics and tree improvement advances of five tropical Pinus species, namely, P. patula, P. oocarpa, P. tecunumanii, P. caribaea, and P. maximinoi, distributed in Mexico, Central America, and the Caribbean. Our objective was to identify and understand the sources of genetic variation in these species. Through a systematic review of five databases comprising a total of two hundred articles, we analyzed the phylogeny, geographic distribution, patterns of variation according to current and future environmental conditions, genomic architecture, and genetic stratification of the species, as well as some results from the improvement programs, including reports of heritability for yield traits. In general, the five species discussed in this chapter have high genetic diversity and large genomes, attributed to abundant repeated regions. Their natural distribution is in the tropical and subtropical zones of Central America, where the genus Pinus exhibits higher species richness and shorter divergence times than the pine species from temperate regions. Furthermore, local heterogeneous climatic and geographic variability enhances local adaptation in these species. Meanwhile, in natural populations there is evidence of greater genetic variability within populations than among populations, indicating rampant gene flow. Despite the lack of information on their complete genomes, pine genetic resources have evolved in parallel to the development of genetic markers, from allozymes and isoenzymes, to RAPD, SSRs, pDNA, nDNA, and more recently to SNPs. Overall, this review compiles the evolutionary history of tropical pines and summarizes the current understanding of genetic diversity in natural tree populations. This standing genetic variation at the population level offers a source of useful variants in terms of diversity, adaptability to climate change, and response to pathogens. Continuing research on the underlying population genetics and adaptive variation in tropical pines will enable advanced schemes of genetic selection capable to integrate evolutionary ecology with tools from the genomics and the quantitative genetics disciplines.