Entomopathogenic nematodes are effective biocontrol agents against arthropod pests. However, their efficacy is limited due to sensitivity to environmental extremes. The objective of the present study was to establish a foundation of genetic-based selection tools for beneficial traits of heat and desiccation tolerance in entomopathogenic nematodes. Screening of natural populations enabled us to create a diverse genetic and phenotypic pool. Gene expression patterns and genomic variation were studied in natural isolates. Heterorhabditis isolates were phenotyped by heat-and desiccation-stress bioassays to determine their survival rates compared to a commercial line. Transcriptomic study was carried out for the commercial line, a high heat-tolerant strain, and for the natural, low heat-tolerant isolate. The results revealed a higher number of upregulated vs. downregulated transcripts in both isolates vs. their respective controls. Functional annotation of the differentially expressed transcripts revealed several known stress-related genes and pathways uniquely expressed. Genome sequencing of isolates with varied degrees of stress tolerance indicated variation among the isolates regardless of their phenotypic characterization. The obtained data lays the groundwork for future studies aimed at identifying genes and molecular markers as genetic selection tools for enhancement of entomopathogenic nematodes ability to withstand environmental stress conditions. Domestication and improvement of crop plants and animals have been part of agriculture for thousands of years. Genetic manipulation of beneficial arthropods, such as silkworms and honeybees, has been conducted for hundreds of years 1,2 and genetic improvement programs have also provided innovative methods for controlling insect pests 3,4. Beneficial arthropods have been selected for climate tolerance 5,6 host-finding ability, host preference 7,8 , improved sex ratio 9,10 , increased fecundity 10,11 , and resistance to insecticides 12,13. Unlike the long history and vast research on the use of beneficial insects for biological control, the use of entomopathogenic nematodes (EPNs) and the genetic improvement of EPNs is in its infancy. As the use of EPNs for biological control of insect pests becomes practical and commercial due to improvements in production methods 14,15 , the use of powerful genetic tools to improve their performance has been strongly advocated (see reviews 16,17). The only free-living stage of the nematode is the third stage infective juvenile (IJ), a non-feeding larva that lives in the soil, and seeks out and penetrates its host through natural openings 18,19. The IJ is exposed to changing environmental conditions and its lack of tolerance to extreme environmental conditions directly influences the shelf life, quality and field performance. Survival, persistence and shelf-life are critical limiting factors for the commercial use of nematodes as biological control agents 20. These difficulties stem mainly from EPNs' sensitivity to heat and desiccation...