© 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Deutschland, ein Teil von Springer Nature.Myrtle (Myrtus communis L.) is a typical plant cover of the Mediterranean region. It is an evergreen perennial shrub or small tree belonging to Myrtaceae family with a natural spread in tropical and subtropical areas. RNA sequencing technique is a common method used to identify transcriptomes. Next-generation sequencing technologies have recently been used for identification and development of SSR markers. This study was conducted to develop SSR markers in myrtle plants with the use of next-generation sequencing technologies. Illumina HiSeq 2000 sequencing device was used for RNA sequencing in two different myrtle genotypes (one with black fruits and the other one with white fruits). RNA-Seq analyses were conducted in two different myrtle genotypes and de novo analyses were performed to identify repeat regions of the genome. Present analyses revealed the greatest repeat pattern as 12,885 di-nucleotide. Number of repeat patterns varied between 12–11,776. Appropriate SSR primers able to amplify these repeat patterns were designed. Within the scope of this study, more than 12,000 SSR primers were developed.