Strongyloidiasis is a much-neglected but sometimes fatal soil born helminthiasis. The causing agent, the small intestinal parasitic nematode
Strongyloides stercoralis
can reproduce sexually through the indirect/heterogonic life cycle, or asexually through the auto-infective or the direct/homogonic life cycles. Usually, among the progeny of the parasitic females both, parthenogenetic parasitic (females only) and sexual free-living (females and males) individuals, are present simultaneously. We isolated
S
.
stercoralis
from people living in a village with a high incidence of parasitic helminths, in particular liver flukes (
Clonorchis sinensis
) and hookworms, in the southern Chinese province Guangxi. We determined nuclear and mitochondrial DNA sequences of individual
S
.
stercoralis
isolated from this village and from close by hospitals and we compared these
S
.
stercoralis
among themselves and with selected published
S
.
stercoralis
from other geographic locations. For comparison, we also analyzed the hookworms present in the same location. We found that, compared to earlier studies of
S
.
stercoralis
populations in South East Asia, all
S
.
stercoralis
sampled in our study area were very closely related, suggesting a recent common source of infection for all patients. In contrast, the hookworms from the same location, while all belonging to the species
Necator americanus
, showed rather extensive genetic diversity even within host individuals. Different from earlier studies conducted in other geographic locations, almost all
S
.
stercoralis
in this study appeared heterozygous for different sequence variants of the 18S rDNA hypervariable regions (HVR) I and IV. In contrast to earlier investigations, except for three males, all
S
.
stercoralis
we isolated in this study were infective larvae, suggesting that the sampled population reproduces predominantly, if not exclusively through the clonal life cycles. Consistently, whole genome sequencing of individual worms revealed higher heterozygosity than reported earlier for likely sexual populations of
S
.
stercoralis
. Elevated heterozygosity is frequently associated with asexual clonal reproduction.