Coffee is the second most valuable commodity exported by developing countries. The Coffea genus comprises over 103 species but coffee production uses only two species throughout the tropics: Coffea canephora, which is self-sterile and diploid and better known as Robusta, and C. arabica, which is self-fertile and tetraploid. With the arrival of new analytical technologies and the start of genome sequencing projects, it was clearly time to review the state of the art of coffee genetics and genomics. In the first part of this chapter, we present the main results concerning genetic diversity and phylogeny – the most advanced fields – based on large molecular marker sets, such as random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), intersimple sequence repeat (ISSR), single sequence repeats (SSRs), or conserved orthologue set (COS), which are mainly polymerase chain reaction (PCR) based. These markers also enable the construction of genetic maps and the identification of quantitative trait loci (QTLs) for both morphological and biochemical traits. In the second part, after reviewing current knowledge on variation in coffee genome size and insights into cytogenetics, we focus on currently available genomic resources and web facilities. Large sets of expressed sequences tags (ESTs) and bacterial artificial chromosome (BAC) libraries for both C. canephora and C. arabica have been obtained along with information on genes and specific metabolic pathways. In the final section, we describe recently designed tools and their ultimate goal, which is to facilitate the sequencing, assembly and annotation of the first Coffea genome. We are at the gate of a new era of scientific approaches to coffee that should lead to a better understanding of phylogenetic relationships and genome evolution within the genus. Finally, taken together, this information should help develop improved varieties to meet the new challenges represented by ongoing radical changes in the environment.