con <- dbConnect(RMySQL::MySQL(), host = "***",dbname="***",user = "***", password = "***")

dbGetQuery(con,"set names utf8")

Q1 <- dbSendQuery(con, "SELECT * FROM cities")

city <- fetch(Q1, n = -1)

> Encoding(city$name) %>% table()
.
unknown
  45734

> Encoding(city$name) <- "UTF-8"
> Encoding(city$name) %>% table()
.
unknown   UTF-8
  44920     814

> library(stringi)
Warning message:
package ‘stringi’ was built under R version 3.3.2
> all(stri_enc_isutf8(city$name))
[1] FALSE

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] stringi_1.1.2 tidyr_0.5.1   purrr_0.2.2   dplyr_0.5.0   RMySQL_0.10.9 DBI_0.4-1

loaded via a namespace (and not attached):
[1] magrittr_1.5   R6_2.1.2       assertthat_0.1 tools_3.3.1    tibble_1.1     Rcpp_0.12.6