Locus   S1  S2  S3
loc1    87  56  77
loc2    34  55  75
loc3    12  09  78
loc4    34  67  89
loc5    78  65  46

Locus   S1  S2  S3
loc3    13  43  34
loc5    43  56  90
loc7    89  56  33
loc1    56  88  00
loc4    66  77  98
loc2    34  44  66

Locus   S1  S2  S3
loc1    56  88  00
loc2    34  44  66
loc3    13  43  34
loc4    66  77  98
loc5    43  56  90

file1 <-read.delim(file="file1.txt",header=TRUE,sep="t")
file2 <-read.delim(file="file2.txt",header=TRUE,sep="t")
new_output <- file1[file1$Locus %in% file2$Locus,]
write.table(new_output,file="new_output.txt",sep="t")

merge(file1["Locus"], file2, by = "Locus")

#  Locus S1 S2 S3
#1  loc1 56 88  0
#2  loc2 34 44 66
#3  loc3 13 43 34
#4  loc4 66 77 98
#5  loc5 43 56 90

new_output <- file2[match(file1$Locus, file2$Locus), ]

file1 <-read.delim(file = "file1.txt", header = TRUE, sep = "t", row.names = 1)
file2 <-read.delim(file = "file2.txt", header = TRUE, sep = "t", row.names = 1)
new_output <- file2[rownames(file1$Locus), ]