Numerous aroma precursor evaluations have been undertaken with green coffee beans of both species of worldwide economic importance: Coffea arabica L. and Coffea canephora P. Efforts have been made to characterise cultivars of these two species. The originality of this study is to present the biochemical diversity of wild accessions originating from Ethiopia and Kenya for C. arabica (38 genotypes) and from five African countries (Côte d'Ivoire, Guinea, Congo, Cameroon and Central African Republik) for C. canephora (38 genotypes). The biochemical aroma parameters assessed by HPLC analysis were: (1) the two alkaloids, caffeine and trigonelline, (2) chlorogenic acids and (3) sucrose. Results reveal that the two species showed significant accession differences for all compounds. Between-species-average-content comparison confirms that C. arabica showed more trigonelline and sucrose and that C. canephora presented more CGA and caffeine. C. canephora diversity was higher than that of C. arabica, except for trigonelline and sucrose. For C. canephora, results showed that: (1) no differences were highlighted between accessions for countries of origin for the alkaloids and sucrose, and (2) the 3-CQA content allowed to accessions to be pooled into two groups.