Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable single molecule, real-time (SMRT) technologies have become available. These offer opportunities to rapidly collect and analyse genomic data anywhere. However, the generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of SMRT offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based SMRT analysis of closely-related plant species (Arabidopsis spp.) has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification-by-sequencing and de novo phylogenomics. Samples were collected and sequenced in a single day by SMRT using a portable, "al fresco" laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with SMRT reads enables rapid and confident species identification. Individually annotated SMRT reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with SMRT and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based SMRT makes real- time, rapid specimen identification and genome wide analyses possible. These technological advances are set to revolutionise research in the biological sciences and have broad implications for conservation, taxonomy, border agencies and citizen science.