The use of advanced molecular methods in plant pathology and applied microbiology has necessitated for more accurate, rapid detection and identification of plant pathogens. This is particularly significant given accelerated emergence of virulence that leads to increased prevalence of plant pathogens. Thus, the capacity to contain plant pathogens and ultimately disease progression is key to ensuring crop biosecurity and overall food security. Of recent, research on pathogens utilizes a holistic approach focusing on elucidating growth dynamics within the entire biome rather than studying individual or closely related isolates in unison. This has advanced knowledge and information of microbial ecosystem within natural environments in the twenty first century. Applied technological platforms used for rapid detection and profiling microbial biomes in this regard include digital PCR, pyrosequencing, Illumina, DNA microarray and barcoding, Ion torrent, and nanopore. These technologies have been applied in various fields including human health and medicine, marine and animal biology, crop production and water quality research, to mention but a few. Although much has been done and achieved through the development of several technologies, more accuracy is required to circumvent the shortfalls still experienced. This includes integrating existing methods with new applications such as viability PCRs and microbial viability testing. Hence, this review provides critical analysis of some widely used latest technologies in rapid detection and identification of plant pathogens, and profiling plant associated microbiomes that reveal growth dynamics and population diversity. The advantages and limitations of the technologies are also discussed.