Consider the following code running in iPython/Jupyter Notebook:

from pandas import *
%matplotlib inline

ys = [[0,1,2,3,4],[4,3,2,1,0]]
x_ax = [0,1,2,3,4]

for y_ax in ys:
    ts = Series(y_ax,index=x_ax)
    ts.plot(kind='bar', figsize=(15,5))

I would expect to have 2 separate plots as output, instead, I get the two series merged in one single plot. Why is that? How can I get two separate plots keeping the for loop?

Just add the call to plt.show() after you plot the graph (you might want to import matplotlib.pyplot to do that), like this:

from pandas import Series
import matplotlib.pyplot as plt
%matplotlib inline

ys = [[0,1,2,3,4],[4,3,2,1,0]]
x_ax = [0,1,2,3,4]

for y_ax in ys:
    ts = Series(y_ax,index=x_ax)
    ts.plot(kind='bar', figsize=(15,5))
    plt.show()