You need a reference to an Axes object to keep drawing on the same subplot.
import matplotlib.pyplot as plt
x = range(100)
y = range(100,200)
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax1.scatter(x[:4], y[:4], s=10, c='b', marker="s", label='first')
ax1.scatter(x[40:],y[40:], s=10, c='r', marker="o", label='second')
plt.legend(loc='upper left');
plt.show()
