Bovine paratuberculosis is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The aims of this study was to investigate the current MAP infection status and MAP transmission risk factors in Taiwan; thereby, to develop a practical control program. A nation-wise survey by serum enzyme linked immunosorbent assay (ELISA) was conducted. Environmental samples from dairy herds were collected for detecting MAP by real time PCR and for phylogenic analysis by variable number tandem repeats (VNTRs). Results indicated that MAP seroprevalence in dairy cow was 10.1%, and 66.7% dairy herds were positive, MAP seroprevalence of beef cattle was 2.8%, MAP seroprevalence of intradermal tuberculin test (ITT) positive cattle was 51.4%. MAP infection status and transmission risk factors are different among different herds. Soil and feces were high risk carries for transmitting MAP. Nine substrains of MAPs were identified indicating direct link of MAP transmission among herds. According to the results above and previous research, a MAP control program was developed.