You need to tell ggplot that you’ve got an ordered factor already, so it doesn’t automatically order it for you.
dat <- read.table(text=
"SC_LTSL_BM 16.8275
SC_STSL_BM 17.3914
proB_FrBC_FL 122.1580
preB_FrD_FL 18.5051
B_Fo_Sp 14.4693
B_GC_Sp 15.4986", header = FALSE, stringsAsFactors = FALSE)
# make V1 an ordered factor
dat$V1 <- factor(dat$V1, levels = dat$V1)
# plot
library(ggplot2)
ggplot(dat,aes(x=V1,y=V2))+geom_bar(stat="identity")