The myrtle rust disease, caused by the fungus Austropuccinia psidii, infects a wide range of host species within the Myrtaceae family worldwide. Since its first report in 2013 in New Caledonia, it was found on various types of native environments where Myrtaceae are the dominant or codominant species, as well as in several commercial nurseries. It is now considered as a significant threat to ecosystems biodiversity and Myrtaceae-related economy. The use of predictive molecular markers for resistance against myrtle rust is currently the most cost-effective and ecological approach to control the disease. Such an approach for neo Caledonian endemic Myrtaceae species was not possible because of the lack of genomic resources. The recent advancement in new generation sequencing technologies accompanied with relevant bioinformatics tools now provide new research opportunity for work in non-model organism at the transcriptomic level. The present study focuses on transcriptome analysis on three Myrtaceae species endemic to New Caledonia (Arillastrum gummiferum, Syzygium longifolium and Tristaniopsis glauca) that display contrasting responses to the pathogen (non-infected vs infected). Differential gene expression (DGE) and variant calling analysis were conducted on each species. We combined a dual approach by using 1) the annotated reference genome of a related Myrtaceae species (Eucalyptus grandis) and 2) a de novo transcriptomes of each species.