ITS and 16S amplicon sequencing data of ten rock samples, colonized by endolithic communities, collected at Joshua Tree National Park (May 2016). The Ribosomal Internal Transcribed Sequence 1 region (ITS1) and V4 region of the 16S rRNA gene were amplified using barcoded ITS1F/ITS2 and F515/R806 primers, respectively, according to Earth Microbiome Project's protocols. Fungal ITS and bacterial 16S primers were made available through the Alfred P. Sloan Foundation Built. Sequencing (2x300 bp) has been performed on Illumina Miseq platform at University of California Riverside (UCR). Data analyses were performed on the High-Performance Computing Cluster at UCR in the Institute of Integrative Genome Biology. The dataset consists of 2 zip archives. Here is a summary of their contents: ITS_fungi: R1.fastq and R2.fastq files 16S_bacteria: R1.fastq and R2.fastq files