Mercury (Hg)-contaminated soil remediation has become an urgent necessity due to its harmful effect on the environment and living organisms. The use of plant-endophyte partnership for phytoremediation demonstrates an excellent opportunity for cleaning heavy metal contaminated soil. This study aimed to screen and characterize the phenotype of the Hg-resistant endophytic bacteria from local grasses (Cynodon dactylon and Eleusine indica) in the Hg-contaminated soil of West Nusa Tenggara, Indonesia with siderophore-producing traits. Siderophore production of bacteria was qualitatively tested using overlay-chrome azurol S (O-CAS) medium and quantitatively tested using the succinic acid medium. The assay was designed using a Completely Randomized Factorial Design consisting of two factors, i.e., isolate type and incubation time with three replicates. The selected isolates were pathogenicity tested, then they were phenotypically and biochemically characterized. All tested isolates showed a positive result on changing O-CAS medium color from blue to yellow/brown that indicated hydroxamate type of siderophore. The highest siderophore production was achieved at 72 hours of incubation, by the EI5 and EI6 isolates (62.90% and 35.31%, respectively). In turn, the CD6, EI5 and EI6 isolates achieved high siderophore production at a short incubation period (48 hours). However, during the hemolysis test, only the CD6 and EI6 isolates were not pathogenic. The CD6 and EI6 isolates would be used for phytoremediation on Hg-contaminated soil in the future study. On the basis of the 16S rDNA analysis, it was shown that the CD6 isolate was Jeotgalicoccus huakuii and the EI6 isolate was Bacillus amyloliquefaciens.