Several studies isolated fungal and bacterial species from extreme environments, such as Sabkha and hot deserts, as their natural habitat, some of which are of medicinal importance. Current research aimed investigating the microbial (fungi and bacteria) diversity and abundance in Sabkha and desert areas in Saudi Arabia. Soil samples from nine different geographical areas (Al-Aushazia lake, AlQasab, AlKasar, Tabuk, Al-Kharj, Al-Madina, Jubail, Taif and Abqaiq) were collected and cultured for microbial isolation. Isolated fungi and bacteria were identified by molecular techniques (PCR and sequencing). Based on 18S rDNA sequencing, 203 fungal species belonging to 33 genera were identified. The most common fungal genera were
Fusarium
,
Alternaria
,
Chaetomium
,
Aspergillus Cochliobolus
and
Pencillium
, while the most common species were
Chaetomium globosum
and
Fusarium oxysporum
. By 16S rDNA sequencing 22 bacterial species belonging to only two genera,
Bacillus
and
Lactobacillus
, were identified. The most commonly isolated bacterial species were
Bacillus subtilis
and
Lactobacillus murinus
. Some fungal species were confined to specific locations, such as
Actinomyces elegans, Fusarium proliferatum, Gymnoascus reesii
and
Myzostoma
spp
.
that were only isolated from Al-Aushazia soil. AlQasab soil had the highest microbial diversity among other areas with abundances of 23.5% and 4.4% of total fungi, and bacteria, respectively. Findings of this study show a higher degree of fungal diversity than that of bacteria in all studied areas. Further studies needed to investigate the connection between some isolated species and their habitat ecology, as well as to identify those of medicinal importance.