The Chemical-bioprospecting is a conceptual, and methodological, tool of singular importance for the evaluation of biodiversity as a sustainable source of metabolites with high added value. In this communication it is reported the strategy of chemical-prospecting, in sustainable and scalable conditions, of Cuban biodiversity, specifically the edaphic fauna and the diplopoda group (Rhinocrycidae-Rhinocricus duvernoyi Karsh 1881), orienting the process towards the isolation of NEE and NEF from defensive secretions. The existence of 5 chemotypes in populations of endemic Cuban millipedes belonging to the species Rhinocricus duvernoyi Karsh 1881 was determined: Yumurí-02 Valley - Isle of Youth (two components, 31/33 and 68/66 % respectively); Alamar-Banao localities (5-9 components with concentrational variations); La Palma (1 component, 100 %); La Coca (mixture of aliphatic hydrocarbons), and Yumurí-01 Valley - Mayarí (quinone, > 80 %). Several novel components were isolated and characterized for this genus (Rhinocricus) and this endemic species of the Cuban archipelago: 1-methyl-2-methoxy-p-quinone, 2-(3,4-dimethoxy-phenyl)-ethylene-1-amine and 4-hydroxy-5-methoxybenzaldehyde (vanillin), as well as polysubstituted phenolic derivatives, which increase the repugnatorial action of these defensive secretions. The work reports a structural-chromatographic database containing the components of defensive secretions and their fragmentation pathways (GC-MS) for geographic populations of the millipede Rhinocricus duvernoyi Karsh inhabiting the western zone of the Cuban archipelago. Its mapping revealed the existence of a singular compositional heterogeneity (5-7 components of aromatic, benzoquinonic and hydrocarbon nature with specific substitution patterns) in the western zone of the Cuban archipelago, allowing the analysis of some ecological and evolutionary considerations for this species and its eco-geographical variations. The cytotoxic, microbiocidal and fungicidal capacity against Gram (-) and Gram (+) pathogenic microorganisms was evaluated, observing a potent biocidal effect, which supported the protocols for the preparation of therapeutic formulations. An eco-sustainable synthetic process of the 1-methyl-2-methoxy-p-quinone derivative with microbiocidal and fungicidal activity was designed, using a non-conventional procedure.