The Chronicles of Yugoha is story told in an anachronic order, meaning that each chapter jumps either forwards or backwards in time at random intervals. Because of that, it might be difficult to tell the relative timing of different episodes. This page lists each chapter in chronological order, as well as with some other dates for the sake of comparison. See the Yu-Gi-Oh Timeline page for my notes on dates used and the dating system.
Before Yugoha (Prior to circa 1,015,000 BYGO)
Circa 1,015,00 BYGO: Chapter 4: Return of Chaos
Age of Yugoha (Circa 1,015,000-15,000 BYGO)
15,021 BYGO: Chapter 1: Birth of a Legend
15,004 BYGO: Chapter 2: What’s in a Name? (Prologue Only)
The Dark Ages (15,000 BYGO-0 BYGO/AYGO)
Era of the First King of Games (0 BYGO/AYGO-100 AYGO)
0.5 AYGO: Chapter 2: What’s in a Name? (Main Episode)
Synchro Era (100-2000 AYGO)
Xyz Era (2000-3000 AYGO)
Pendulum Era (3000-4,000 AYGO)
Evolution Era (4,000-5,002 AYGO)
The Return of Yugoha (5,002 AYGO-Present)
5,003 AYGO: Episode 3: God Killers
Yu-Gi-Oh! Millennium The Official Website 