Coccidiosis, caused by the Eimeria species, greatly affects the poultry industry. Severity of the disease varies depending
on the identity of the infecting parasites, encouraging identification of Eimeria species circulating on a farm as a valuable
component of chicken management. Conventional methods of Eimeria species identification are time consuming and
can be subjective in nature. Given these limitations, molecular approaches have been developed for specific detection of
Eimeria species. In this study, faecal samples were collected from commercial broiler farms and subjected to microscopic
examination for Eimeria occurrence. Eimeria species were putatively identified by morphological characterisation and
grouped into three categories based on oocyst size. Molecular detection of Eimeria species occurrence in these samples
was then performed using two published PCR assays (the individual components of a SCAR-based multiplex PCR, and
assays developed for quantitative PCR, termed PCR-SCAR 1 and PCR-SCAR 2 here) and a LAMP assay. Comparison of the
results obtained demonstrated that the three molecular methods were capable of detecting all Eimeria species of the
reference Houghton strain, but showed varying efficiencies in detecting Malaysian field isolates. PCR-SCAR 2 was found
to be the most effective, detecting all seven Eimeria species and indicating the presence of Eimeria parasites in most
flocks. Differences in the ability of the molecular methods to detect Eimeria may be a consequence of sequence divergence
between isolates from different regions, implying that development of region-specific methods using local Eimeria strains
may be required to improve the efficiency of molecular assays for Eimeria detection