I want to know whether my 2nd paper containing different regions in the same gene (for example mtDNA COI) as a molecular marker can be viewed as repetitive publication?
The short answer is "whatever the referee thinks is repetitive publication". In my experience, if the referee raises the issue, then it's very hard to convince the editors to accept the paper even if you can make a very clear case that it isn't serial publication. If the referee doesn't care, then it's not an issue.
Experts in your area can give you an idea of how likely a referee is to think that your case would raise questions. But since it comes down to the opinion of one or two individuals, it can be very unpredictable. There may be cases where specific journals have detailed rules about this, but I haven't seen anything like that in my area (physics).