The present study recorded the population of the goby fish (Perciformes: Gobiidae),
Eutaeniichthys
cf.
gilli
Jordan & Snyder, 1901, from the tunnel burrowed by the mud shrimp
Austinogebia edulis
Ngo-Ho and Chan, 1992 in a mudflat in Shengang and Wangong of Changhua County, western Taiwan. This finding is not only a new record of the genus in Taiwan, it is also the first record of this species in a mudflat near an industrial park. In total, 56 individuals of
E
. cf.
gilli
were collected from June 2016 to September 2018. Morphological traits of males and females were measured. The resin casting method trapped bodies of
E
. cf.
gilli
that were present in the tunnel burrow and proved that the fish inhabits burrows of the mud shrimp
A
.
edulis
. In addition, a species of snapping shrimp was also found in the same tunnel. Symbiotic interaction may occur between
E
. cf.
gilli
,
A
.
eduli
and the snapping shrimp. The China Coastal Current (CCC) runs along the coastlines of Japan, Korea, China, and reaches western Taiwan during the northeast monsoon period. The CCC, therefore, might play an important role in the biogeographic distribution of
E
. cf.
gilli
in the western Pacific Ocean. Since
E
. cf.
gilli
is listed in the Red List as an endangered species of Japan for many years, Taiwan waters may provide a refuge for this fish species warranting a broader investigation. Since Taiwan is some distance away from the previously recorded locations in Japan, Korea, the Yellow Sea, and the Bohai Sea, a phylogenic analysis is warranted for population and species differentiation in the future.